12 papers · ranked by Valyu relevance
Ghanshyam Chandra, Md Helal Hossen, Stephan Scholz, Alexander T Dilthey + 2 more
Affordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference genome is unreliable in highly polymorphic and repetitive regions, further…
Valerio Galanti, Lingting Shi, Elham Azizi, Yining Liu + 1 more
Single-cell RNA sequencing has transformed the field of cellular biology by providing unprecedented insights into cellular heterogeneity. However, characterizing scRNA-seq datasets remains a significant challenge. We introduce RefCM, a novel computational method that combines optimal transport and integer programming…
Mengzhen Guo, Stefan Grünewald
We present Lpnet, a variant of the widely used Neighbor-net method that approximates pairwise distances between taxa by a circular phylogenetic network. We first apply standard methods to construct a binary phylogenetic tree and then use integer linear programming to compute an optimal circular orderings that agrees…
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…
Virgile Andreani, Eric J. South, Mary J. Dunlop
Dense arrangements of binding sites within nucleotide sequences can collectively influence downstream transcription rates or initiate biomolecular interactions. For example, natural promoter regions can harbor many overlapping transcription factor binding sites that influence the rate of transcription initiation.…
Olesya Melnichenko, Venkat S. Malladi
In the field of genomics, bioinformatics pipelines play a crucial role in processing and analyzing vast biological datasets. These pipelines, consisting of interconnected tasks, can be optimized for efficiency and scalability by leveraging cloud platforms such as Microsoft Azure. The choice of compute resources…
Conor F. Hayes, Steven A. Magana-Zook, Andre Gonçalves, Ahmet Can Solak + 2 more
We propose a novel approach for antibody library design that combines deep learning and multi-objective linear programming with diversity constraints. Our method leverages recent advances in sequence and structure-based deep learning for protein engineering to predict the effects of mutations on antibody properties.…
Fernando H. C. Dias, Alexandru I. Tomescu
Minimum flow decomposition (MFD) is a common problem across various fields of Computer Science, where a flow is decomposed into a minimum set of weighted paths. However, in Bioinformatics applications, such as RNA transcript or quasi-species assembly, the flow is erroneous, since is obtained from noisy read coverages.…
Henri Schmidt, Benjamin J. Raphael
Reconstructing unobserved ancestral states of a phylogenetic tree provides insight into the history of evolving systems and is one of the fundamental problems in phylogenetics. For a fixed phylogenetic tree, the most parsimonious ancestral reconstruction – a solution to the small parsimony problem – can be efficiently…
Pouya Ahadi, Balabhaskar Balasundaram, Juan S. Borrero, Charles Chen
In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic…
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…
Aaryan M. Sarnaik, Ke Chen, Austin Diaz, Mingfu Shao
Reducing into a satisfiability (SAT) formulation has been proven effective in solving certain NP-hard problems. In this work, we extend this research by presenting a novel SAT formulation for computing the double-cut-and-join (DCJ) distance between two genomes with duplicate genes. The DCJ distance serves as a crucial…