Search · four archives
Search · four archives
6 papers · ranked by Valyu relevance
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…
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…
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…
Benjamin M. David, Paul A. Jensen
Coordinating multiple liquid handling robots is a complex logistical task when designing biological experiments. Protocol designers must consider the capabilities and constraints of each robot to distribute work optimally across multiple instruments. We developed an optimization framework that finds optimal liquid…