11 papers · ranked by Valyu relevance
Barış Ekim, Bonnie Berger, Yaron Orenstein
As the volume of next generation sequencing data increases, an urgent need for algorithms to efficiently process the data arises. Universal hitting sets (UHS) were recently introduced as an alternative to the central idea of minimizers in sequence analysis with the hopes that they could more efficiently address common…
Grant Ongo, Sébastien G. Ricoult, Timothy E. Kennedy, David Juncker
Cell navigation is directed by inhomogeneous distributions of extracellular cues. It is well known that noise plays a key role in biology and is present in naturally occurring gradients at the micro- and nanoscale, yet it has not been studied with gradients in vitro. Here, we introduce novel algorithms to produce…
Miaoshan Lu, Hengxuan Jiang, Ruimin Wang, Shaowei An + 2 more
Plate Design is a necessary and time-consuming operation for GC/LC-MS based sample preparation. The implementation of the inter-batch balancing algorithm and the intra-batch randomization algorithm can have a significant impact on the final analysis results. For researchers without programming skills, a stable and…
Mahmudur Rahman Hera, David Koslicki, Conrado Martínez
With the surge in sequencing data generated from an ever-expanding range of biological studies, designing scalable computational techniques has become essential. One effective strategy to enable large-scale computation is to split long DNA or protein sequences into k-mers, and summarize large k-mer sets into compact…
Ragnar Groot Koerkamp, Giulio Ermanno Pibiri
Given a string S, a minimizer scheme is an algorithm defined by a triple (k, w, 𝒪) that samples a subset of k-mers (k-long substrings) from a string S. Specifically, it samples the minimal k-mer according to the order 𝒪 from each window of w consecutive k-mers in S. Because consecutive windows can sample the same…
Dogan Corus, Duc-Cuong Dang, Anton V. Eremeev, Per Kristian Lehre
Understanding how the time-complexity of evolutionary algorithms (EAs) depend on their parameter settings and characteristics of fitness landscapes is a fundamental problem in evolutionary computation. Most rigorous results were derived using a handful of key analytic techniques, including drift analysis. However…
Arjun Chandrasekhar, Deborah M. Gordon, Saket Navlakha
We study how the arboreal turtle ant (Cephalotes goniodontus) solves a fundamental computing problem: maintaining a trail network and finding alternative paths to route around broken links in the network. Turtle ants form a routing backbone of foraging trails linking several nests together. This species travels only in…
Tung Dang, Hirohisa Kishino
Random forest (RF) captures complex feature patterns that differentiate groups of samples and is rapidly being adopted in microbiome studies. However, a major challenge is the high dimensionality of microbiome datasets. They include thousands of species or molecular functions of particular biological interest. This…
Prasad U. Bandodkar, Razeen R. Shaikh, Gregory T. Reeves
Model development is essential to gain a mathematical understanding of the underlying phenomena in systems biology. In most models, it is typically hard to estimate the values of the biophysical/phenomenological parameters that characterize the model. The parameters are estimated by minimizing a function that reduces a…
James R. H. Cooke, Luc P. J. Selen, Robert J. van Beers, W. Pieter Medendorp
Comparing models facilitates testing different hypotheses regarding the computational basis of perception and action. Effective model comparison requires stimuli for which models make different predictions. Typically, experiments use a predetermined set of stimuli or sample stimuli randomly. Both methods have…
Yaniv Erlich, Anna Gilbert, Hung Ngo, Atri Rudra + 4 more
Molecular biology increasingly relies on large screens where enormous numbers of specimens are systematically assayed in the search for a particular, rare outcome. These screens include the systematic testing of small molecules for potential drugs and testing the association between genetic variation and a phenotype of…