Manda Riehl
YOU?
Author Swipe
View article: The R-loop grammar predicts R-loop formation under different topological constraints
The R-loop grammar predicts R-loop formation under different topological constraints Open
R-loops are transient three-stranded nucleic acids that form during transcription when the nascent RNA hybridizes with the template DNA, freeing the non-template strand of the DNA. There is growing evidence that R-loops play important role…
View article: Accessibility of Modified NK Fitness Landscapes
Accessibility of Modified NK Fitness Landscapes Open
In this paper we present two modifications of traditional NK fitness landscapes, the θNK and HNK models, and explore these modifications via accessibility and ruggedness. The θNK model introduces a parameter θ to integrate local Rough Moun…
View article: The R-loop Grammar predicts R-loop formation under different topological constraints
The R-loop Grammar predicts R-loop formation under different topological constraints Open
R-loops are transient three-stranded nucleic acids that form during transcription when the nascent RNA hybridizes with the template DNA, freeing the DNA non-template strand. There is growing evidence that R-loops play important roles in ph…
View article: Predicting the stability of profiling signals of small RNAs
Predicting the stability of profiling signals of small RNAs Open
Profiling is a process that finds similarities between different RNA secondary structures by extracting signals from the Boltzmann sampling. The reproducibility of profiling can be identified by the standard deviation of number of features…
View article: The Deletion-Insertion model applied to the genome rearrangement problem
The Deletion-Insertion model applied to the genome rearrangement problem Open
Permutations are frequently used in solving the genome rearrangement problem, whose goal is finding the shortest sequence of mutations transforming one genome into another. We introduce the Deletion-Insertion model (DI) to model small-scal…
View article: A bijection between the set of nesting-similarity classes and L & P matchings
A bijection between the set of nesting-similarity classes and L & P matchings Open
Matchings are frequently used to model RNA secondary structures; however, not all matchings can be realized as RNA motifs. One class of matchings, called the L $\&$ P matchings, is the most restrictive model for RNA secondary structures in…
View article: A bijection between the set of nesting-similarity classes and L & P matchings
A bijection between the set of nesting-similarity classes and L & P matchings Open
Matchings are frequently used to model RNA secondary structures; however, not all matchings can be realized as RNA motifs. One class of matchings, called the L $\&$ P matchings, is the most restrictive model for RNA secondary structure…
View article: Pattern avoiding linear extensions of rectangular posets
Pattern avoiding linear extensions of rectangular posets Open
Inspired by Yakoubov's 2015 investigation of pattern avoiding linear extensions of the posets called combs, we study pattern avoiding linear extensions of rectangular posets. These linear extensions are closely related to standard tableaux…
View article: Pattern avoidance in forests of binary shrubs
Pattern avoidance in forests of binary shrubs Open
We investigate pattern avoidance in permutations satisfying some additional restrictions. These are naturally considered in terms of avoiding patterns in linear extensions of certain forest-like partially ordered sets, which we call binary…
View article: Pattern Avoidance in Task-Precedence Posets
Pattern Avoidance in Task-Precedence Posets Open
We have extended classical pattern avoidance to a new structure: multiple task-precedence posets whose Hasse diagrams have three levels, which we will call diamonds. The vertices of each diamond are assigned labels which are compatible wit…
View article: Generating Functions and Wilf Equivalence for Generalized Interval Embeddings
Generating Functions and Wilf Equivalence for Generalized Interval Embeddings Open
In 1999 in [J. Difference Equ. Appl. 5, 355–377], Noonan and Zeilberger extended the Goulden-Jackson Cluster Method to find generating functions of word factors. Then in 2009 in [Electron. J. Combin. 16(2), RZZ], Kitaev, Liese, Remmel and …
View article: Pattern Avoidance in k-ary Heaps
Pattern Avoidance in k-ary Heaps Open
In this paper, we consider pattern avoidance in k-ary heaps, where the permutation associated with the heap is found by recording the nodes as they are encountered in a breadth-first search. We enumerate heaps that avoid patterns of length…