Search · four archives
Search · four archives
9 papers · ranked by Valyu relevance
Giovanni Stracquadanio, Kun Yang, Jef D. Boeke, Romain Koszul + 1 more
Yeast SCRaMbLE is an experimental method using designed synthetic yeast chromosomes to generate combinatorial diversity through genome rearrangements. These events occur at designed loxPsym recombination sites through the activity of Cre recombinase. While the synthetic SCRaMbLE system was designed to explore minimal…
Joshua K. Peeples, Julie F. Jameson, Nisha M. Kotta, Jonathan M. Grasman + 2 more
We quantify adipose tissue deposition at surgical sites as a function of biomaterial implantation. To our knowledge, this study is the first investigation to apply convolutional neural network (CNN) models to identify and segment adipose tissue in histological images from silk fibroin biomaterial implants. When…
Avijeet Kulshrestha, Sudeep N Punnathanam, K Ganapathy Ayappa
The transition of an α-helix to a β-sheet in proteins is among the most complex conformational changes seen in bio-molecular systems. Currently, it is difficult to study such protein conformational changes in a direct molecular dynamics simulation. This limitation is typically overcome using an indirect approach…
Sarwan Ali, Haris Mansoor, Prakash Chourasia, Murray Patterson
Biological sequence classification is vital in various fields, such as genomics and bioinformatics. The advancement and reduced cost of genomic sequencing have brought the attention of researchers for protein and nucleotide sequence classification. Traditional approaches face limitations in capturing the intricate…
Ross J. Burton, Simone M. Cuff, Matt P. Morgan, Andreas Artemiou + 1 more
Clustering is an unsupervised method for identifying structure in unlabelled data. In the context of cytometry, is typically used to categorise cells into subpopulations of similar phenotype. However, clustering is greatly dependent on hyperparameters and the data to which it is applied as each algorithm makes…
Efthymios Oikonomou, Thomas Gruber, Achanta Ravi Chandra, Sarina Höller + 3 more
The power of single-channel patch-clamp recordings is widely acknowledged among ion channel enthusiasts. The method allows observing the action of a single protein complex in real time and hence the deduction of the underlying conformational changes in the ion channel protein. Commonly, recordings are modeled using…
Andrei Ciuparu, Raul C. Mureșan
We introduce Gradient-k, an upgrade of the k-means algorithm that improves clustering accuracy and reduces the number of iterations required for convergence. This is achieved by correcting the distance used in the k-means algorithm by a factor based on the angle between the density gradient and the direction to the…
Yunheng Han, Erin K. Molloy
Summary methods are widely used to reconstruct species trees from gene trees while accounting for incomplete lineage sorting; however, it is increasingly recognized that their accuracy can be negatively impacted by incomplete and/or error-ridden gene trees. To address the latter, 60 leverage gene tree branch lengths…
Fatemeh Hadaeghi, Kayson Fakhar, Claus C. Hilgetag
We introduce efficient Network Reciprocity Control (NRC) algorithms for steering the degree of asymmetry and reciprocity in binary and weighted networks while preserving fundamental network properties. Our methods maintain edge density in binary networks and cumulative edge weight in weighted graphs. We test these…