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A. Zelikovsky · SciRah

Researcher profile · Semantic Scholar

A. Zelikovsky

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A. Zelikovsky — researcher profile on SciRah

h-index: 46
Works: 291
Citations: 8,475

Most-cited papers

Eleven grand challenges in single-cell data science
David Lähnemann, J. Köster, Ewa Szczurek, Davis J. McCarthy +47 more
2020Genome Biology1,272 citations Open access
Semantic Scholar
Systematic benchmarking of omics computational tools
S. Mangul, Lana S. Martin, Brian L. Hill, Angela Ka-Mei Lam +4 more
2019Nature Communications138 citations Open access
Semantic Scholar
Technology dictates algorithms: recent developments in read alignment
Mohammed Alser, Jeremy Rotman, Dhrithi Deshpande, K. Taraszka +13 more
2020Genome Biology136 citations Open access
Semantic Scholar
Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction
S. Knyazev, Viachaslau Tsyvina, A. Shankar, Andrew Melnyk +8 more
2018bioRxiv64 citations Open access
Semantic Scholar
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data
P. Skums, A. Zelikovsky, Rahul Singh, Walker Gussler +12 more
2018Bioinform.61 citations Open access
Semantic Scholar
Bootstrap-based differential gene expression analysis for RNA-Seq data with and without replicates
Sahar Al Seesi, Y. T. Tiagueu, A. Zelikovsky, I. Măndoiu
2014BMC Genomics61 citations Open access
Semantic Scholar
Accurate viral population assembly from ultra-deep sequencing data
S. Mangul, Nicholas C. Wu, N. Mancuso, A. Zelikovsky +2 more
2014Bioinform.57 citations Open access
Semantic Scholar
ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching
Igor Mandric, A. Zelikovsky
2015Annual International Conference on Research in Computational Molecular Biology56 citations Open access
Semantic Scholar
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era
S. Knyazev, Lauren Hughes, P. Skums, A. Zelikovsky
2020Briefings Bioinform.55 citations Open access
Semantic Scholar
Sensory nerves impede the formation of tertiary lymphoid structures and development of protective anti-melanoma immune responses
K. Vats, O. Kruglov, Bikram Sahoo, Vishal Soman +8 more
2022Cancer immunology research53 citations Open access
Semantic Scholar
Fast bootstrapping‐based estimation of confidence intervals of expression levels and differential expression from RNA‐Seq data
Igor Mandric, Yvette Temate-Tiagueu, T. Shcheglova, Sahar Al Seesi +2 more
2017Bioinform.50 citations Open access
Semantic Scholar
Unlocking capacities of genomics for the COVID-19 response and future pandemics
S. Knyazev, Karishma Chhugani, V. Sarwal, Ram Ayyala +31 more
2022Nature Methods48 citations Open access
Semantic Scholar
Benchmarking of computational error-correction methods for next-generation sequencing data
Keith Mitchell, J. Brito, Igor Mandric, Qiaozhen Wu +22 more
2020Genome Biology36 citations Open access
Semantic Scholar
Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows
P. Skums, N. Mancuso, Alexander Artyomenko, Bassam Tork +3 more
2013BMC Bioinformatics35 citations Open access
Semantic Scholar
Global transmission network of SARS-CoV-2: from outbreak to pandemic
P. Skums, Alexander S. Kirpich, P. Baykal, A. Zelikovsky +1 more
2020medRxiv30 citations Open access
Semantic Scholar
Efficient Approximate Kernel Based Spike Sequence Classification
Sarwan Ali, Bikram Sahoo, Muhammad Asad Khan, A. Zelikovsky +2 more
2022IEEE/ACM Transactions on Computational Biology & Bioinformatics27 citations Open access
Semantic Scholar
Inference of genetic relatedness between viral quasispecies from sequencing data
O. Glebova, S. Knyazev, Andrew Melnyk, Alexander Artyomenko +3 more
2017BMC Genomics26 citations Open access
Semantic Scholar
Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants
Alexander Artyomenko, Nicholas C. Wu, S. Mangul, E. Eskin +2 more
2016bioRxiv25 citations Open access
Semantic Scholar
Searching High-Order SNP Combinations for Complex Diseases Based on Energy Distribution Difference
Xiaojun Ding, Jian-Xin Wang, A. Zelikovsky, Xuan Guo +2 more
2015IEEE/ACM Transactions on Computational Biology & Bioinformatics23 citations
Semantic Scholar
Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms
Fengpan Zhao, P. Skums, A. Zelikovsky, Eric L. Sevigny +4 more
2020IEEE/ACM Transactions on Computational Biology & Bioinformatics22 citations
Semantic Scholar
Transcriptome assembly and quantification from Ion Torrent RNA-Seq data
S. Mangul, Sahar Al Seesi, I. Măndoiu, A. Caciula +2 more
2013BMC Genomics20 citations Open access
Semantic Scholar
Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections
Pelin B. Icer Baykal, J. Lara, Y. Khudyakov, A. Zelikovsky +1 more
2020bioRxiv19 citations Open access
Semantic Scholar
Inference of clonal selection in cancer populations using single-cell sequencing data
P. Skums, Viachaslau Tsyvina, A. Zelikovsky
2018bioRxiv19 citations Open access
Semantic Scholar
Antibody Response to Lyme Disease Spirochetes in the Context of VlsE-Mediated Immune Evasion
Artem S. Rogovskyy, D. C. Gillis, Y. Ionov, Ekaterina Gerasimov +1 more
2016Infection and Immunity15 citations Open access
Semantic Scholar
Inferring metabolic pathway activity levels from RNA-Seq data
Yvette Temate-Tiagueu, Sahar Al Seesi, Meril Mathew, Igor Mandric +7 more
2016BMC Genomics15 citations Open access
Semantic Scholar
From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering
Andrew Melnyk, Fatemeh Mohebbi, S. Knyazev, Bikram Sahoo +4 more
2021bioRxiv14 citations Open access
Semantic Scholar
Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling
P. Skums, Alexander Artyomenko, O. Glebova, S. Ramachandran +5 more
2015Bioinform.14 citations Open access
Semantic Scholar
12 Grand Challenges in Single-Cell Data Science
David Lähnemann, J. Köster, Ewa Szczurek, Davis J. McCarthy +47 more
2019PeerJ Preprints13 citations Open access
Semantic Scholar
Using earth mover’s distance for viral outbreak investigations
Andrew Melnyk, S. Knyazev, F. Vannberg, L. Bunimovich +2 more
2019BMC Genomics13 citations Open access
Semantic Scholar
Influence of symbiont-produced bioactive natural products on holobiont fitness in the marine bryozoan, Bugula neritina via protein kinase C (PKC)
Meril Mathew, Kayla I. Bean, Yvette Temate-Tiagueu, A. Caciula +3 more
201612 citations
Semantic Scholar
Clustering Based Identification of SARS-CoV-2 Subtypes
Andrew Melnyk, Fatemeh Mohebbi, S. Knyazev, Bikram Sahoo +4 more
2020International Conference on Computational Advances in Bio and Medical Sciences11 citations
Semantic Scholar
Identification of Surface Epitopes Associated with Protection against Highly Immune-Evasive VlsE-Expressing Lyme Disease Spirochetes
Maliha Batool, S. Caoili, L. Dangott, Ekaterina Gerasimov +5 more
2018Infection and Immunity10 citations Open access
Semantic Scholar
Repeat aware evaluation of scaffolding tools
Igor Mandric, S. Knyazev, A. Zelikovsky, B. Berger
2017bioRxiv10 citations Open access
Semantic Scholar
GaussianCpG: a Gaussian model for detection of CpG island in human genome sequences
Ning Yu, Xuan Guo, A. Zelikovsky, Yi Pan
2017BMC Genomics9 citations Open access
Semantic Scholar
HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads
S. Mangul, T. Yang, Farhad Hormozdiari, Alexandra Dainis +4 more
2016bioRxiv9 citations Open access
Semantic Scholar
Computational Methods for Next Generation Sequencing Data Analysis
I. Măndoiu, A. Zelikovsky
20169 citations
Semantic Scholar
ILP-based maximum likelihood genome scaffolding
James Lindsay, Hamed Salooti, I. Măndoiu, A. Zelikovsky
2014BMC Bioinformatics9 citations Open access
Semantic Scholar
Identifying Biomarkers Using Support Vector Machine to Understand the Racial Disparity in Triple-Negative Breast Cancer
Bikram Sahoo, Zandra Pinnix, Seth Sims, A. Zelikovsky
2023J. Comput. Biol.8 citations Open access
Semantic Scholar
kGEM: An EM-based algorithm for local reconstruction of viral quasispecies
Alexander Artyomenko, N. Mancuso, A. Zelikovsky, P. Skums +1 more
2013International Conference on Computational Advances in Bio and Medical Sciences8 citations
Semantic Scholar
Analysis of heterogeneous genomic samples using image normalization and machine learning
S. Basodi, P. Baykal, A. Zelikovsky, P. Skums +1 more
2019BMC Genomics6 citations Open access
Semantic Scholar
Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire
Ekaterina Gerasimov, A. Zelikovsky, I. Măndoiu, Y. Ionov
2015International Conference on Computational Advances in Bio and Medical Sciences6 citations Open access
Semantic Scholar
Delineating Surface Epitopes of Lyme Disease Pathogen Targeted by Highly Protective Antibodies of New Zealand White Rabbits
Artem S. Rogovskyy, S. Caoili, Y. Ionov, H. Piontkivska +4 more
2019Infection and Immunity5 citations Open access
Semantic Scholar
Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants
Viachaslau Tsyvina, David S. Campo, Seth Sims, A. Zelikovsky +2 more
2018BMC Bioinformatics5 citations Open access
Semantic Scholar
A Study of Optimal Cost-Skew Tradeoff and Remaining Suboptimality in Interconnect Tree Constructions
Kwangsoo Han, A. Kahng, C. Moyes, A. Zelikovsky
2018International Workshop on System-Level Interconnect Prediction5 citations
Semantic Scholar
Practical Approximations of Steiner Trees in Uniform Orientation Metrics
I. Măndoiu, A. Kahng, A. Zelikovsky
2018Handbook of Approximation Algorithms and Metaheuristics5 citations
Semantic Scholar
VGA: A method for viral quasispecies assembly from ultra-deep sequencing data
S. Mangul, Nicholas C. Wu, N. Mancuso, A. Zelikovsky +2 more
2014International Conference on Computational Advances in Bio and Medical Sciences5 citations
Semantic Scholar
Inference of mutability landscapes of tumors from single cell sequencing data
Viachaslau Tsyvina, A. Zelikovsky, S. Snir, P. Skums
2020PLoS Comput. Biol.4 citations Open access
Semantic Scholar
New Zealand White Rabbits Effectively Clear Borrelia burgdorferi B31 despite the Bacterium’s Functional vlsE Antigenic Variation System
Maliha Batool, A. Hillhouse, Y. Ionov, K. Kochan +7 more
2019Infection and Immunity4 citations Open access
Semantic Scholar
QoS Multimedia Multicast Routing
I. Măndoiu, A. Olshevsky, A. Zelikovsky
2018Handbook of Approximation Algorithms and Metaheuristics4 citations
Semantic Scholar
Metabolic Analysis of Metatranscriptomic Data from Planktonic Communities
Igor Mandric, S. Knyazev, C. Padilla, F. Stewart +2 more
2017International Symposium on Bioinformatics Research and Applications4 citations
Semantic Scholar

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I. Măndoiu×16
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