Alex Zelikovsky

71 papers B 4Misc 1Journal 27Unranked 37

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Editorial: Special Section on Computational Advances in Bio and Medical Sciences. IEEE Trans. Comput. Biol. Bioinform. Ion I. Mandoiu, Marmar R. Moussa, Sanguthevar Rajasekaran, Pavel Skums, Sharma V. Thankachan, Alex Zelikovsky
2024	—	`conf`	Machine Learning-Driven Discovery of Quadruple-Negative Breast Cancer Subtypes from Gene Expression Data. ISBRA (1) Bikram Sahoo, Nikita Jinna, Padmashree Rida, Zandra Pinnix, Alex Zelikovsky
2023	—	`conf`	Decoding Heterogeneity in Quadruple-Negative Breast Cancer: A Data-driven Clustering Approach. ICCABS Bikram Sahoo, Nikita Jinna, Padmashree Rida, Zandra Pinnix, Alex Zelikovsky
2023	—	`conf`	Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer. ISBRA Bikram Sahoo, Zandra Pinnix, Alex Zelikovsky
2023	—	`conf`	Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection Algorithms. ISBRA Bikram Sahoo, Temitope Adeyeha, Zandra Pinnix, Alex Zelikovsky
2023	—	`conf`	Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire. ISBRA Hossein Saghaian, Pavel Skums, Yurij Ionov, Alex Zelikovsky
2023	J	`jnl`	Identifying Biomarkers Using Support Vector Machine to Understand the Racial Disparity in Triple-Negative Breast Cancer. J. Comput. Biol. Bikram Sahoo, Zandra Pinnix, Seth Sims, Alex Zelikovsky
2023	J	`jnl`	Reconstruction of Viral Variants via Monte Carlo Clustering. J. Comput. Biol. Akshay Juyal, Roya Hosseini, Daniel Novikov, Mark Grinshpon, Alex Zelikovsky
2022	J	`jnl`	Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms. IEEE ACM Trans. Comput. Biol. Bioinform. Fengpan Zhao, Pavel Skums, Alex Zelikovsky, Eric L. Sevigny, Monica Haavisto Swahn, Sheryl M. Strasser, Yan Huang, Yubao Wu
2022	—	`conf`	Entropy Based Clustering of Viral Sequences. ISBRA Akshay Juyal, Roya Hosseini, Daniel Novikov, Mark Grinshpon, Alex Zelikovsky
2021	—	`conf`	A Novel Network Representation of SARS-CoV-2 Sequencing Data. ISBRA 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
2021	—	`ed.`	Computational Advances in Bio and Medical Sciences - 10th International Conference, ICCABS 2020, Virtual Event, December 10-12, 2020, Revised Selected Papers ICCABS Sumit Kumar Jha, Ion I. Mandoiu, Sanguthevar Rajasekaran, Pavel Skums, Alex Zelikovsky
2021	J	`jnl`	From Alpha to Zeta: Identifying Variants and Subtypes of SARS-CoV-2 Via Clustering. J. Comput. Biol. Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson
2021	J	`jnl`	Scalable Reconstruction of SARS-CoV-2 Phylogeny with Recurrent Mutations. J. Comput. Biol. Daniel Novikov, Sergey Knyazev, Mark Grinshpon, Pelin B. Icer, Pavel Skums, Alex Zelikovsky
2020	—	`conf`	Benchmarking of computational error-correction methods for next-generation sequencing data. BCB 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
2020	—	`conf`	Clustering Based Identification of SARS-CoV-2 Subtypes. ICCABS Andrew Melnyk, Fatemeh Mohebbi, Sergey Knyazev, Bikram Sahoo, Roya Hosseini, Pavel Skums, Alex Zelikovsky, Murray Patterson
2020	—	`conf`	Estimating Enzyme Participation in Metabolic Pathways for Microbial Communities from RNA-seq Data. ISBRA Filipp Rondel, Roya Hosseini, Bikram Sahoo, Sergey Knyazev, Igor Mandric, Frank Stewart, Ion I. Mandoiu, Bogdan Pasaniuc, Alex Zelikovsky
2020	J	`jnl`	Inference of mutability landscapes of tumors from single cell sequencing data. PLoS Comput. Biol. Viachaslau Tsyvina, Alex Zelikovsky, Sagi Snir, Pavel Skums
2019	J	`jnl`	12 Grand Challenges in Single-Cell Data Science. PeerJ Prepr. 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
2019	—	`conf`	Detecting Illicit Drug Ads in Google+ Using Machine Learning. ISBRA Fengpan Zhao, Pavel Skums, Alex Zelikovsky, Eric L. Sevigny, Monica Haavisto Swahn, Sheryl M. Strasser, Yubao Wu
2019	J	`jnl`	Inference of clonal selection in cancer populations using single-cell sequencing data. Bioinform. Pavel Skums, Viachaslau Tsyvina, Alex Zelikovsky
2018	—	`conf`	A study of optimal cost-skew tradeoff and remaining suboptimality in interconnect tree constructions. SLIP@DAC Kwangsoo Han, Andrew B. Kahng, Christopher Moyes, Alex Zelikovsky
2018	J	`jnl`	Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants. BMC Bioinform. Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums
2018	—	`conf`	Predicting Opioid Epidemic by Using Twitter Data. ISBRA Yubao Wu, Pavel Skums, Alex Zelikovsky, David Stiven Campo Rendon, Xueting Liao
2018	J	`jnl`	QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data. Bioinform. 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
2018	J	`jnl`	Repeat-aware evaluation of scaffolding tools. Bioinform. Igor Mandric, Sergey Knyazev, Alex Zelikovsky
2017	—	`conf`	Agent-Based in Silico Evolution of HCV Quasispecies. ISBRA Alexander Artyomenko, Pelin B. Icer, Pavel Skums, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky
2017	—	`conf`	Assessment of HCV infection stage as recent or chronic using multi-parameter analysis and machine learning. ICCABS Pelin Icer Baykal, Alexander Artyomenko, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky, Pavel Skums
2017	—	`conf`	Efficient filtering algorithm for detection of genetic similarity between large genomic datasets. ICCABS Viachaslau Tsyvina, David S. Campo, Seth Sims, Alex Zelikovsky, Yury Khudyakov, Pavel Skums
2017	J	`jnl`	Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data. Bioinform. Igor Mandric, Yvette Temate-Tiagueu, Tatiana Shcheglova, Sahar Al Seesi, Alex Zelikovsky, Ion I. Mandoiu
2017	J	`jnl`	Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire. BMC Bioinform. Ekaterina Gerasimov, Alex Zelikovsky, Ion I. Mandoiu, Yurij Ionov
2017	J	`jnl`	Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. J. Comput. Biol. Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
2017	—	`conf`	Metabolic Analysis of Metatranscriptomic Data from Planktonic Communities. ISBRA Igor Mandric, Sergey Knyazev, Cory Padilla, Frank Stewart, Ion I. Mandoiu, Alex Zelikovsky
2017	—	`conf`	Modeling the Spread of HIV and HCV Infections Based on Identification and Characterization of High-Risk Communities Using Social Media. ISBRA Deeptanshu Jha, Pavel Skums, Alex Zelikovsky, Yury Khudyakov, Rahul Singh
2016	—	`ed.`	Bioinformatics Research and Applications - 12th International Symposium, ISBRA 2016, Minsk, Belarus, June 5-8, 2016, Proceedings ISBRA Anu G. Bourgeois, Pavel Skums, Xiang Wan, Alex Zelikovsky
2016	—	`conf`	HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads. ISBRA Serghei Mangul, Harry (Taegyun) Yang, Farhad Hormozdiari, Elizabeth Tseng, Alex Zelikovsky, Eleazar Eskin
2016	B	`conf`	Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. RECOMB Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
2015	—	`conf`	2SNV: Quasispecies reconstruction from PacBio reads. ICCABS Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky
2015	—	`conf`	Algorithms for prediction of viral transmission using analysis of intra-host viral populations. ICCABS Pavel Skums, Olga Glebova, David S. Campo, Nana Li, Zoya Dimitrova, Seth Sims, Leonid Bunimovich, Alex Zelikovsky, Yury Khudyakov
2015	J	`jnl`	Computational framework for next-generation sequencing of heterogeneous viral populations using combinatorial pooling. Bioinform. Pavel Skums, Alexander Artyomenko, Olga Glebova, Sumathi Ramachandran, Ion I. Mandoiu, David S. Campo, Zoya Dimitrova, Alex Zelikovsky, Yuri Khudyakov
2015	—	`conf`	Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire. ICCABS Ekaterina Nenastyeva, Alex Zelikovsky, Yurij Ionov, Ion I. Mandoiu
2015	B	`conf`	ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching. RECOMB Igor Mandric, Alex Zelikovsky
2015	J	`jnl`	ScaffMatch: scaffolding algorithm based on maximum weight matching. Bioinform. Igor Mandric, Alex Zelikovsky
2015	J	`jnl`	Searching High-Order SNP Combinations for Complex Diseases Based on Energy Distribution Difference. IEEE ACM Trans. Comput. Biol. Bioinform. Xiaojun Ding, Jianxin Wang, Alex Zelikovsky, Xuan Guo, Minzhu Xie, Yi Pan
2014	J	`jnl`	Accurate viral population assembly from ultra-deep sequencing data. Bioinform. Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin
2014	Misc	`ed.`	Computing and Combinatorics - 20th International Conference, COCOON 2014, Atlanta, GA, USA, August 4-6, 2014. Proceedings COCOON Zhipeng Cai, Alex Zelikovsky, Anu G. Bourgeois
2014	—	`conf`	Detection of genetic relatedness between viral samples using EM-based clustering of next-generation sequencing data. ICCABS Pavel Skums, Alexander Artyomenko, Olga Glebova, Alex Zelikovsky, David S. Campo, Zoya Dimitrova, Yuri Khudyakov
2014	—	`conf`	Deterministic regression algorithm for transcriptome frequency estimation. ICCABS Adrian Caciula, Olga Glebova, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky
2014	—	`conf`	Reconstruction of influenza a virus variants from PacBio reads. ICCABS Alexander Artyomenko, Serghei Mangul, Nicholas C. Wu, Eleazar Eskin, Ren Sun, Alex Zelikovsky
2014	—	`conf`	SILP3: Maximum likelihood approach to scaffolding. ICCABS Igor Mandric, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky
2014	—	`conf`	VGA: A method for viral quasispecies assembly from ultra-deep sequencing data. ICCABS Serghei Mangul, Nicholas C. Wu, Nicholas Mancuso, Alex Zelikovsky, Ren Sun, Eleazar Eskin
2013	—	`conf`	Alignment of DNA Mass-Spectral Profiles Using Network Flows. ISBRA Pavel Skums, Olga Glebova, Alex Zelikovsky, Zoya Dimitrova, David Stiven Campo Rendon, Lilia Ganova-Raeva, Yuri Khudyakov
2013	—	`conf`	Estimation of viral population structure from amplicon-based reads. ICCABS Nicholas Mancuso, Alexander Artyomenko, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu
2013	—	`conf`	Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq data. ICCABS Adrian Caciula, Alex Zelikovsky, Serghei Mangul, James Lindsay, Ion I. Mandoiu
2013	—	`conf`	Optimizing pooling strategies for the massive next-generation sequencing of viral samples. ICCABS Pavel Skums, Olga Glebova, Alex Zelikovsky, Ion I. Mandoiu, Yuri Khudyakov
2013	J	`jnl`	Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows. BMC Bioinform. Pavel Skums, Nicholas Mancuso, Alexander Artyomenko, Bassam Tork, Ion I. Mandoiu, Yuri Khudyakov, Alex Zelikovsky
2013	—	`conf`	Reference assisted nucleic acid sequence reconstruction from mass spectrometry data. ICCABS Gabriel Ilie, Alex Zelikovsky, Ion I. Mandoiu
2013	—	`conf`	Transcriptome assembly and quantification from Ion Torrent RNA-Seq data. ICCABS Serghei Mangul, Sahar Al Seesi, Ion I. Mandoiu, Adrian Caciula, Alex Zelikovsky, Dumitru Brinza
2013	—	`conf`	kGEM: An EM-based algorithm for local reconstruction of viral quasispecies. ICCABS Alexander Artyomenko, Nicholas Mancuso, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu
2012	J	`jnl`	Efficient error correction for next-generation sequencing of viral amplicons. BMC Bioinform. Pavel Skums, Zoya Dimitrova, David S. Campo, Gilberto Vaughan, Livia Rossi, Joseph C. Forbi, Jonny Yokosawa, Alex Zelikovsky, Yuri Khudyakov
2012	J	`jnl`	Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations. Silico Biol. Serghei Mangul, Adrian Caciula, Olga Glebova, Ion I. Mandoiu, Alex Zelikovsky
2012	J	`jnl`	Reconstructing viral quasispecies from NGS amplicon reads. Silico Biol. Nicholas Mancuso, Bassam Tork, Pavel Skums, Lilia Ganova-Raeva, Ion I. Mandoiu, Alex Zelikovsky
2012	J	`jnl`	TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads. BMC Bioinform. Serghei Mangul, Adrian Caciula, Dumitru Brinza, Ion I. Mandoiu, Alex Zelikovsky
2011	—	`conf`	Collaborative Topology Control for Lifetime Maximization. MSN Lei Shi, Wen-Zhan Song, Mingsen Xu, Alex Zelikovsky, Li Yu
2011	J	`jnl`	Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol. Biol. Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky
2011	J	`jnl`	Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinform. Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu, Peter Balfe, Alex Zelikovsky
2010	—	`conf`	Estimation of alternative splicing isoform frequencies from RNA-Seq data. Structure Discovery in Biology: Motifs, Networks & Phylogenies Marius Nicolae, Serghei Mangul, Ion I. Mandoiu, Alex Zelikovsky
2009	B	`conf`	Scheduling Bursts Using Interval Graphs in Optical Burst Switching Networks. GLOBECOM Xiaojun Cao, Yichuan Wang, Alex Zelikovsky
2006	—	`conf`	Multiple Linear Regression for Index SNP Selection on Unphased Genotypes. EMBC Jingwu He, Alex Zelikovsky
2005	B	`conf`	Node caching enhancement of reactive ad hoc routing protocols [MANET]. WCNC Sunsook Jung, Nisar Hundewale, Alex Zelikovsky
2002	J	`jnl`	A note on the colorability of mixed hypergraph using k colors. Comput. Sci. J. Moldova Dmitrii Lozovanu, Vitaly I. Voloshin, Alex Zelikovsky