155 citations · 164 across the 9 of their papers we have counts for
11 papers
2-Adic Tree Embeddings: A Modeling and Optimization Framework for Computational Phylogenetics
Pavel Skums
Phylogenetic inference is a fundamental problem in computational biology, with applications ranging from epidemiology and oncology to developmental biology and comparative genomics…
SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities
Viorel Munteanu, Michael A. Saldana, David Dreifuss +29
During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient viral surveillance tool that takes into account asymptomatic cases and can iden…
Antigenic cooperation in Viral Populations: Transformation of Functions of Intra-Host Viral Variants
Leonid Bunimovich, Athulya Ram, Pavel Skums
In this paper we study intra-host viral adaptation by antigenic cooperation - a mechanism of immune escape that serves as an alternative to the standard mechanism of escape by cont…
Unlocking capacities of viral genomics for the COVID-19 pandemic response
Sergey Knyazev, Karishma Chhugani, Varuni Sarwal +19
More than any other infectious disease epidemic, the COVID-19 pandemic has been characterized by the generation of large volumes of viral genomic data at an incredible pace due to…
Scale-free spanning trees: complexity, bounds and algorithms
Yury Orlovich, Kirill Kukharenko, Volker Kaibel +1
We introduce and study the general problem of finding a most "scale-free-like" spanning tree of a connected graph. It is motivated by a particular problem in epidemiology, and may…
Technology dictates algorithms: Recent developments in read alignment
Mohammed Alser, Jeremy Rotman, Kodi Taraszka +13
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. M…
Graph fractal dimension and structure of fractal networks: a combinatorial perspective
Pavel Skums, Leonid Bunimovich
In this paper we study self-similar and fractal networks from the combinatorial perspective. We establish analogues of topological (Lebesgue) and fractal (Hausdorff) dimensions for…
Graph Hausdorff dimension, Kolmogorov complexity and construction of fractal graphs
Leonid Bunimovich, Pavel Skums
In this paper we introduce and study discrete analogues of Lebesgue and Hausdorff dimensions for graphs. It turned out that they are closely related to well-known graph characteris…
Krausz dimension and its generalizations in special graph classes
Olga Glebova, Yury Metelsky, Pavel Skums
A {\it krausz -partition} of a graph is the partition of into cliques, such that any vertex belongs to at most cliques and any two cliques have at most verti…
-product and -threshold graphs
Pavel Skums
This paper is the continuation of the research of the author and his colleagues of the {\it canonical} decomposition of graphs. The idea of the canonical decomposition is to define…
Reconstruction of p-disconnected graphs
Pavel Skums
We prove that Kelly-Ulam conjecture is true for p-disconnected graphs.