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Assessing the Potential of Gene Tree Parsimony for Microbial Phylogenomics
A key challenge in microbial phylogenomics is that microbial gene families are often affected by extensive horizontal gene transfer (HGT). As a...
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Evidence of Increased Adaptation of Omicron SARS-CoV-2 Codons to Humans
Viruses are highly dependent on their hosts to carry out cellular mechanisms and cause productive infection. Thus, they undergo extensive adaptations...
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Revisiting the Effects of MDR1 Variants Using Computational Approaches
P-glycoprotein, encoded by the MDR1 gene, is an ATP-dependent pump that exports various substances out of cells. Its overexpression is related to...
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Maximum Alternating Balanced Cycle Decomposition and Applications in Sorting by Intergenic Operations Problems
In the literature on genome rearrangement, several approaches use different structures to improve the results of genome rearrangement problems. In...
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Gene Tree Parsimony in the Presence of Gene Duplication, Loss, and Incomplete Lineage Sorting
Inferring species trees from multi-locus data needs to account for gene tree discordance due to various biological processes, including incomplete...
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Gene-Adjacency-Based Phylogenetics Under a Stochastic Gain-Loss Model
A key task in molecular systematics is to decipher the evolutionary history of strains of a species. Standard markers are often too crude in this...
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REvolutionH-tl: Reconstruction of Evolutionary Histories tool
Orthology detection from sequence similarity remains a difficult and computationally expensive problem for gene families with large numbers of gene...
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On the Distribution of Synteny Blocks Under a Neutral Model of Genome Dynamics
Prokaryotes are a rich source of versatile molecular functional systems that typically consist of multiple, interacting proteins. The study of such...
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Galled Perfect Transfer Networks
Predicting horizontal gene transfers often requires comparative sequence data, but recent work has shown that character-based approaches could also...
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Comparative Genomics 21st International Conference, RECOMB-CG 2024, Boston, MA, USA, April 27–28, 2024, Proceedings
This book constitutes the proceedings of the 21st International Conference on Comparative Genomics, RECOMB-CG 2024, which was held in Boston, MA,...
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Inferring Transcript Phylogenies from Transcript Ortholog Clusters
Alternative Splicing (AS) is a mechanism in eukaryotic gene expression by which different combinations of introns are spliced to produce distinct...
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Sampling Gene Adjacencies and Geodesic Points of Random Genomes
The breakpoint distance employed in comparative genomics is not a geodesic distance, which makes it difficult to study genomes (i.e. permutations)...
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Transcription Factors Across the Escherichia coli Pangenome: A 3D Perspective
Identification of complete sets of transcription factors (TFs) is a foundational step in the inference of genetic regulatory networks. The...
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Statistically Consistent Estimation of Rooted and Unrooted Level-1 Phylogenetic Networks from SNP Data
We address the problem of estimating a rooted phylogenetic network, as well as its unrooted version, from SNPs (i.e., single nucleotide...
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Mathematical Optimization Theory and Operations Research: Recent Trends 22nd International Conference, MOTOR 2023, Ekaterinburg, Russia, July 2–8, 2023, Revised Selected Papers
This book constitutes refereed proceedings of the 22nd International Conference on Mathematical Optimization Theory and Operations Research: Recent...
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String Processing and Information Retrieval 30th International Symposium, SPIRE 2023, Pisa, Italy, September 26–28, 2023, Proceedings
This volume LNCS 14240 constitutes the refereed proceedings of the 30th International Symposium on String Processing and Information Retrieval, SPIRE...
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Optimization Algorithms for Distributed Machine Learning
This book discusses state-of-the-art stochastic optimization algorithms for distributed machine learning and analyzes their convergence speed. The...
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Transactions on Computational Science XL
The LNCS journal Transactions on Computational Science reflects recent developments in the field of Computational Science, conceiving the field not...
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Quantized and Sparsified Distributed SGD
The communication delay in sending and receiving gradients or model updates between the worker nodes and the parameter server can be significantly,...
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Asynchronous SGD and Staleness-Reduced Variants
In Chap. we saw that synchronous distributed SGD suffers from tail latency due to straggling workers. Its straggler-resilient variants K-sync and...