12 papers · ranked by Valyu relevance
Frans Zdyb, Julius B. Kirkegaard
Biological image and video analysis is full of discrete decisions: whether an object is present, which multi-hypothesis detections are real, whether two detections are tracking the same object, or whether a cell divides or not. Standard pipelines resolve these locally and in sequence, e.g through non-max suppression…
Hugo Magalhães, Jonas Weber, Gunnar W. Klau, Tobias Marschall + 1 more
Variation of sequence copy number (CN) between individuals can be associated with phenotypical differences. Consequently, CN calling is an important step for disease association and identification, as well as for genome assembly validation. Traditionally, CN calling is done by mapping sequencing reads to a linear…
Xinyu Gu, Stefan Ivanovic, Daniel W. Feng, Mohammed El-Kebir
Summarizing a collection P of related RNA secondary structures is a key challenge in applications like evolutionary analysis, alternative fold studies and mRNA vaccine design. This requires both clustering the input structures into similar groups and identifying the core structural motifs on which they agree or differ.…
Kexin Niu, Maxat Kulmanov, Robert Hoehndorf
Current machine learning methods for enzyme function prediction primarily treat proteins as independent entities, ignoring the metabolic context in which they operate. This reductionist approach often generates biologically implausible annotations that fail to satisfy stoichiometric or thermodynamic constraints. While…
Ke Chen, Abhishek Talesara, Sanchal Thakkar, Mingfu Shao
The minimum flow decomposition problem abstracts a set of key tasks in bioinformatics, including metagenome and transcriptome assembly. These tasks, collectively known as multi-assembly, aim to reconstruct multiple genomic sequences from reads obtained from mixed samples. The reads are first organized into a directed…
Arseny Shur, Ido Tziony, Yaron Orenstein
Minimizers are sampling schemes which are ubiquitous in almost any high-throughput sequencing analysis. Assuming a fixed alphabet of size σ, a minimizer is defined by two positive integers k, w and a linear order ρ on k-mers. A sequence is processed by a sliding window algorithm that chooses in each window of length w…
Qinghui Zhou, Seyed Pouria Ahmadi, Ibrahim Numanagić
Accurate genotyping and phasing of highly polymorphic gene families are essential for precision medicine. Yet, the genotyping problem remains computationally challenging due to extreme sequence similarity between related genes, copy number variation, and structural complexity. Current methods typically rely on integer…
Jing Xie, Qi Duan
Biological pathway analysis often requires identifying interventions that block reachability to an undesirable state, such as a disease-associated module, toxic byproduct, or adverse phenotype, while preserving reachability among essential biological functions. Motivated by this setting, we study the Reachability…
Timo N. Schneider, Florence Stoffel, Marco A. Bühler, Karolína Mrzílková + 2 more
Many biological proteins can assemble into dynamic, non-stoichiometric structures known as biomolecular condensates. Although typically observed at micrometer scales in vitro, recent evidence shows that these condensates often appear as nanoscale assemblies both in vitro and in cells. Moreover, biochemical reactions…
Ghanshyam Chandra, William T. Doan, Daniel Gibney
Genotyping is the task of identifying the genetic variants present in a sample from sequencing data, and it is a fundamental problem in computational biology. Existing genotyping approaches typically rely on either haplotype reference panels or pangenome graphs. Compared to haplotype reference panels, pangenome graphs…
A.J.R. Cotter
A simulator, ‘ECOLPS’ in R, is developed and trialed for ecological studies of closed aquatic ecosystems. Its constraint-based approach contrasts with function-based models widely applied in ecology. Total gross production (ΣGP) by ‘wild components’ (= species/life stages, grouped by ecological roles) is maximized…
Dhruv D. Jatkar, M. Ali Al-Radhawi, Christopher A. Voigt, Eduardo D. Sontag
Implementing logic functions in living cells is a fundamental area of interest among synthetic biologists. The goal of designing biochemical circuits in synthetic biology is to make modular and tractable systems that perform well with predictable behaviors. Developing formalisms towards the design of such systems has…