Alex Zelikovsky

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 33

Top Topics

Social Media Platforms

Grand Challenges

Top Venues

J. Comput. Biol.

Publications

Bikram Sahoo, Nikita Jinna, Padmashree Rida, Zandra Pinnix, Alex Zelikovsky
Machine Learning-Driven Discovery of Quadruple-Negative Breast Cancer Subtypes from Gene Expression Data. ISBRA (1) (2024)
Akshay Juyal, Roya Hosseini, Daniel Novikov, Mark Grinshpon, Alex Zelikovsky
Reconstruction of Viral Variants via Monte Carlo Clustering. J. Comput. Biol. 30 (9) (2023)
Hossein Saghaian, Pavel Skums, Yurij Ionov, Alex Zelikovsky
Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire. ISBRA (2023)
Bikram Sahoo, Zandra Pinnix, Alex Zelikovsky
Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer. ISBRA (2023)
Bikram Sahoo, Zandra Pinnix, Seth Sims, Alex Zelikovsky
Identifying Biomarkers Using Support Vector Machine to Understand the Racial Disparity in Triple-Negative Breast Cancer. J. Comput. Biol. 30 (4) (2023)
Bikram Sahoo, Temitope Adeyeha, Zandra Pinnix, Alex Zelikovsky
Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection Algorithms. ISBRA (2023)
Akshay Juyal, Roya Hosseini, Daniel Novikov, Mark Grinshpon, Alex Zelikovsky
Entropy Based Clustering of Viral Sequences. ISBRA (2022)
Fengpan Zhao, Pavel Skums, Alex Zelikovsky, Eric L. Sevigny, Monica Haavisto Swahn, Sheryl M. Strasser, Yan Huang, Yubao Wu
Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Daniel Novikov, Sergey Knyazev, Mark Grinshpon, Pelin B. Icer, Pavel Skums, Alex Zelikovsky
Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations. J. Comput. Biol. 28 (11) (2021)
Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson
From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering. J. Comput. Biol. 28 (11) (2021)
Sergey Knyazev, Daniel Novikov, Mark Grinshpon, Harman Singh, Ram Ayyala, Varuni Sarwal, Roya Hosseini, Pelin Icer Baykal, Pavel Skums, Ellsworth Campbell, Serghei Mangul, Alex Zelikovsky
A Novel Network Representation of SARS-CoV-2 Sequencing Data. ISBRA (2021)
Viachaslau Tsyvina, Alex Zelikovsky, Sagi Snir, Pavel Skums
Inference of mutability landscapes of tumors from single cell sequencing data. PLoS Comput. Biol. 16 (11) (2020)
Filipp Rondel, Akram Sadat Hosseini, Bikram Sahoo, Sergey Knyazev, Igor Mandric, Frank Stewart, Ion I. Mandoiu, Bogdan Pasaniuc, Alex Zelikovsky
Estimating Enzyme Participation in Metabolic Pathways for Microbial Communities from RNA-seq Data. ISBRA (2020)
Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson
Clustering Based Identification of SARS-CoV-2 Subtypes. ICCABS (2020)
Keith Mitchell, Jaqueline J. Brito, Igor Mandric, Qiaozhen Wu, Sergey Knyazev, Sei Chang, Lana S. Martin, Aaron Karlsberg, Ekaterina Gerasimov, Russell Littman, Brian L. Hill, Nicholas C. Wu, Harry (Taegyun) Yang, Kevin Hsieh, Linus Chen, Eli Littman, Taylor Shabani, German Enik, Douglas Yao, Ren Sun, Jan Schroeder, Eleazar Eskin, Alex Zelikovsky, Pavel Skums, Mihai Pop, Serghei Mangul
Benchmarking of computational error-correction methods for next-generation sequencing data. BCB (2020)
Fengpan Zhao, Pavel Skums, Alex Zelikovsky, Eric L. Sevigny, Monica Haavisto Swahn, Sheryl M. Strasser, Yubao Wu
Detecting Illicit Drug Ads in Google+ Using Machine Learning. ISBRA (2019)
Pavel Skums, Viachaslau Tsyvina, Alex Zelikovsky
Inference of clonal selection in cancer populations using single-cell sequencing data. Bioinform. 35 (14) (2019)
David Laehnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Niko Beerenwinkel, Kieran R. Campbell, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn A. Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P. F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Lukasz Raczkowski, Marcel J. T. Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth
12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 7 (2019)
Yubao Wu, Pavel Skums, Alex Zelikovsky, David Stiven Campo Rendon, Xueting Liao
Predicting Opioid Epidemic by Using Twitter Data. ISBRA (2018)
Pavel Skums, Alex Zelikovsky, Rahul Singh, Walker Gussler, Zoya Dimitrova, Sergey Knyazev, Igor Mandric, Sumathi Ramachandran, David S. Campo, Deeptanshu Jha, Leonid Bunimovich, Elizabeth Costenbader, Connie Sexton, Siobhán O'Connor, Guo-liang Xia, Yury Khudyakov
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. Bioinform. 34 (1) (2018)
Kwangsoo Han, Andrew B. Kahng, Christopher Moyes, Alex Zelikovsky
A study of optimal cost-skew tradeoff and remaining suboptimality in interconnect tree constructions. SLIP@DAC (2018)
Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums
Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants. BMC Bioinform. (11) (2018)
Igor Mandric, Sergey Knyazev, Alex Zelikovsky
Repeat-aware evaluation of scaffolding tools. Bioinform. 34 (15) (2018)
Pelin Icer Baykal, Alexander Artyomenko, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky, Pavel Skums
Assessment of HCV infection stage as recent or chronic using multi-parameter analysis and machine learning. ICCABS (2017)
Deeptanshu Jha, Pavel Skums, Alex Zelikovsky, Yury Khudyakov, Rahul Singh
Modeling the Spread of HIV and HCV Infections Based on Identification and Characterization of High-Risk Communities Using Social Media. ISBRA (2017)
Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. J. Comput. Biol. 24 (6) (2017)
Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums
Efficient filtering algorithm for detection of genetic similarity between large genomic datasets. ICCABS (2017)
Igor Mandric, Yvette Temate-Tiagueu, Tatiana Shcheglova, Sahar Al Seesi, Alex Zelikovsky, Ion I. Mandoiu
Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data. Bioinform. 33 (20) (2017)
Alexander Artyomenko, Pelin B. Icer, Pavel Skums, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky
Agent-Based in Silico Evolution of HCV Quasispecies. ISBRA (2017)
Ekaterina Gerasimov, Alex Zelikovsky, Ion I. Mandoiu, Yurij Ionov
Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire. BMC Bioinform. 18 (8) (2017)
Igor Mandric, Sergey Knyazev, Cory Padilla, Frank Stewart, Ion I. Mandoiu, Alex Zelikovsky
Metabolic Analysis of Metatranscriptomic Data from Planktonic Communities. ISBRA (2017)
Serghei Mangul, Harry (Taegyun) Yang, Farhad Hormozdiari, Elizabeth Tseng, Alex Zelikovsky, Eleazar Eskin
HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads. ISBRA (2016)
Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. RECOMB (2016)
Igor Mandric, Alex Zelikovsky
ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching. RECOMB (2015)
Igor Mandric, Alex Zelikovsky
ScaffMatch: scaffolding algorithm based on maximum weight matching. Bioinform. 31 (16) (2015)
Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
2SNV: Quasispecies reconstruction from PacBio reads. ICCABS (2015)
Pavel Skums, Olga Glebova, David S. Campo, Nana Li, Zoya Dimitrova, Seth Sims, Leonid Bunimovich, Alex Zelikovsky, Yury Khudyakov
Algorithms for prediction of viral transmission using analysis of intra-host viral populations. ICCABS (2015)
Ekaterina Nenastyeva, Alex Zelikovsky, Yurij Ionov, Ion I. Mandoiu
Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire. ICCABS (2015)
Xiaojun Ding, Jianxin Wang, Alex Zelikovsky, Xuan Guo, Minzhu Xie, Yi Pan
Searching High-Order SNP Combinations for Complex Diseases Based on Energy Distribution Difference. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (3) (2015)
Pavel Skums, Alexander Artyomenko, Olga Glebova, Sumathi Ramachandran, Ion I. Mandoiu, David S. Campo, Zoya Dimitrova, Alex Zelikovsky, Yuri Khudyakov
Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. Bioinform. 31 (5) (2015)
Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin
Accurate viral population assembly from ultra-deep sequencing data. Bioinform. 30 (12) (2014)
Pavel Skums, Alexander Artyomenko, Olga Glebova, Alex Zelikovsky, David S. Campo, Zoya Dimitrova, Yuri Khudyakov
Detection of genetic relatedness between viral samples using EM-based clustering of next-generation sequencing data. ICCABS (2014)
Alexander Artyomenko, Serghei Mangul, Nicholas C. Wu, Eleazar Eskin, Ren Sun, Alex Zelikovsky
Reconstruction of influenza a virus variants from PacBio reads. ICCABS (2014)
Adrian Caciula, Olga Glebova, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky
Deterministic regression algorithm for transcriptome frequency estimation. ICCABS (2014)
Igor Mandric, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky
SILP3: Maximum likelihood approach to scaffolding. ICCABS (2014)
Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin
VGA: A method for viral quasispecies assembly from ultra-deep sequencing data. ICCABS (2014)
Alexander Artyomenko, Nicholas Mancuso, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu
kGEM: An EM-based algorithm for local reconstruction of viral quasispecies. ICCABS (2013)
Pavel Skums, Nicholas Mancuso, Alexander Artyomenko, Bassam Tork, Ion I. Mandoiu, Yuri Khudyakov, Alex Zelikovsky
Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows. BMC Bioinform. 14 (S-9) (2013)
Nicholas Mancuso, Alexander Artyomenko, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu
Estimation of viral population structure from amplicon-based reads. ICCABS (2013)
Pavel Skums, Olga Glebova, Alex Zelikovsky, Zoya Dimitrova, David Stiven Campo Rendon, Lilia Ganova-Raeva, Yuri Khudyakov
Alignment of DNA Mass-Spectral Profiles Using Network Flows. ISBRA (2013)
Gabriel Ilie, Alex Zelikovsky, Ion I. Mandoiu
Reference assisted nucleic acid sequence reconstruction from mass spectrometry data. ICCABS (2013)
Serghei Mangul, Sahar Al Seesi, Ion I. Mandoiu, Adrian Caciula, Alex Zelikovsky, Dumitru Brinza
Transcriptome assembly and quantification from Ion Torrent RNA-Seq data. ICCABS (2013)
Pavel Skums, Olga Glebova, Alex Zelikovsky, Ion I. Mandoiu, Yuri Khudyakov
Optimizing pooling strategies for the massive next-generation sequencing of viral samples. ICCABS (2013)
Adrian Caciula, Alex Zelikovsky, Serghei Mangul, James Lindsay, Ion I. Mandoiu
Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq data. ICCABS (2013)
Serghei Mangul, Adrian Caciula, Dumitru Brinza, Ion I. Mandoiu, Alex Zelikovsky
TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads. BMC Bioinform. 13 (S-18) (2012)
Nicholas Mancuso, Bassam Tork, Pavel Skums, Lilia Ganova-Raeva, Ion I. Mandoiu, Alex Zelikovsky
Reconstructing viral quasispecies from NGS amplicon reads. Silico Biol. 11 (5-6) (2012)
Serghei Mangul, Adrian Caciula, Olga Glebova, Ion I. Mandoiu, Alex Zelikovsky
Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations. Silico Biol. 11 (5-6) (2012)
Pavel Skums, Zoya Dimitrova, David S. Campo, Gilberto Vaughan, Livia Rossi, Joseph C. Forbi, Jonny Yokosawa, Alex Zelikovsky, Yuri Khudyakov
Efficient error correction for next-generation sequencing of viral amplicons. BMC Bioinform. 13 (S-10) (2012)
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky
Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol. Biol. 6 (2011)
Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alex Zelikovsky
Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinform. 12 (S-6) (2011)
Lei Shi, Wen-Zhan Song, Mingsen Xu, Alex Zelikovsky, Li Yu
Collaborative Topology Control for Lifetime Maximization. MSN (2011)
Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky
Estimation of alternative splicing isoform frequencies from RNA-Seq data. Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)
Xiaojun Cao, Yichuan Wang, Alex Zelikovsky
Scheduling Bursts Using Interval Graphs in Optical Burst Switching Networks. GLOBECOM (2009)
Jingwu He, Alex Zelikovsky
Multiple Linear Regression for Index SNP Selection on Unphased Genotypes. EMBC (2006)
Sunsook Jung, Nisar Hundewale, Alex Zelikovsky
Node caching enhancement of reactive ad hoc routing protocols [MANET]. WCNC (2005)
Dmitrii Lozovanu, Vitaly I. Voloshin, Alex Zelikovsky
A note on the colorability of mixed hypergraph using k colors. Comput. Sci. J. Moldova 10 (1) (2002)