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Alexander Zelikovsky
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- affiliation: Georgia State University, Department of Computer Science
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2020 – today
- 2023
[j93]Mukul S. Bansal, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky:
Special Issue: 11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021). J. Comput. Biol. 30(4): 363-365 (2023)- [j92]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): 502-517 (2023) - [j91]Zhipeng Cai, Pavel Skums, Alexander Zelikovsky:
Special Issue, Part I 18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022). J. Comput. Biol. 30(8): 829-830 (2023) - [j90]Akshay Juyal, Roya Hosseini, Daniel Novikov, Mark Grinshpon, Alex Zelikovsky:
Reconstruction of Viral Variants via Monte Carlo Clustering. J. Comput. Biol. 30(9): 1009-1018 (2023) - [c136]Hossein Saghaian, Pavel Skums, Yurij Ionov, Alex Zelikovsky:
Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire. ISBRA 2023: 214-226 - [c135]Hafsa Farooq, Daniel Novikov, Akshay Juyal, Alexander Zelikovsky:
Genetic Algorithm with Evolutionary Jumps. ISBRA 2023: 453-463 - [c134]Bikram Sahoo, Temitope Adeyeha, Zandra Pinnix, Alex Zelikovsky:
Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection Algorithms. ISBRA 2023: 487-497 - [c133]Bikram Sahoo, Zandra Pinnix, Alex Zelikovsky:
Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer. ISBRA 2023: 498-508 - [c132]Zahra Tayebi, Akshay Juyal, Alexander Zelikovsky, Murray Patterson:
Simulating Tumor Evolution from scDNA-Seq as an Accumulation of both SNVs and CNAs. ISBRA 2023: 530-540 - [e10]Xuan Guo, Serghei Mangul, Murray Patterson, Alexander Zelikovsky:
Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Wrocław, Poland, October 9-12, 2023, Proceedings. Lecture Notes in Computer Science 14248, Springer 2023, ISBN 978-981-99-7073-5 [contents] - 2022
- [j89]Zhipeng Cai, Pavel Skums, Alexander Zelikovsky:
17th International Symposium on Bioinformatics Research and Applications (ISBRA 2021). J. Comput. Biol. 29(10): 1059-1060 (2022) - [j88]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): 180-191 (2022) - [c131]Akshay Juyal, Roya Hosseini, Daniel Novikov, Mark Grinshpon, Alex Zelikovsky:
Entropy Based Clustering of Viral Sequences. ISBRA 2022: 369-380 - [i12]Sarwan Ali, Bikram Sahoo, Muhammad Asad Khan, Alexander Zelikovsky, Imdadullah Khan, Murray Patterson:
Efficient Approximate Kernel Based Spike Sequence Classification. CoRR abs/2209.04952 (2022) - 2021
- [j87]Sergey Knyazev, Lauren Hughes, Pavel Skums, Alexander Zelikovsky:
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era. Briefings Bioinform. 22(1): 96-108 (2021) - [j86]Ion I. Mandoiu, T. M. Murali, Giri Narasimhan, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky:
Special Issue: 9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019). J. Comput. Biol. 28(2): 115-116 (2021) - [j85]Zhipeng Cai, Pavel Skums, Yuri Porozov, Alexander Zelikovsky:
Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020). J. Comput. Biol. 28(7): 636 (2021) - [j84]Zhipeng Cai, Pavel Skums, Yuri Porozov, Alexander Zelikovsky:
Special Issue: 16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020). J. Comput. Biol. 28(8): 745-746 (2021) - [j83]Filipp Rondel, Roya Hosseini, Bikram Sahoo, Sergey Knyazev, Igor Mandric, Frank Stewart, Ion I. Mandoiu, Bogdan Pasaniuc, Yuri Porozov, Alexander Zelikovsky:
Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data. J. Comput. Biol. 28(8): 842-855 (2021) - [j82]Sumit Kumar Jha, Ion I. Mandoiu, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky:
Special Issue: 10th International Computational Advances in Bio and Medical Sciences (ICCABS 2020). J. Comput. Biol. 28(11): 1033-1034 (2021) - [j81]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): 1113-1129 (2021) - [j80]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): 1130-1141 (2021) - [c130]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: 165-175 - [e9]Sumit Kumar Jha, Ion I. Mandoiu, Sanguthevar Rajasekaran, Pavel Skums, Alex Zelikovsky:
Computational Advances in Bio and Medical Sciences - 10th International Conference, ICCABS 2020, Virtual Event, December 10-12, 2020, Revised Selected Papers. Lecture Notes in Computer Science 12686, Springer 2021, ISBN 978-3-030-79289-3 [contents] - 2020
- [j79]Zhipeng Cai, Pavel Skums, Alexander Zelikovsky:
Preface Special Issue: 15th International Symposium on Bioinformatics Research and Applications (ISBRA 2019). J. Comput. Biol. 27(2): 131-132 (2020) - [j78]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) - [c129]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: 63:1 - [c128]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: 127-141 - [c127]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: 335-343 - [e8]Ion I. Mandoiu, T. M. Murali, Giri Narasimhan, Sanguthevar Rajasekaran, Pavel Skums, Alexander Zelikovsky:
Computational Advances in Bio and Medical Sciences - 9th International Conference, ICCABS 2019, Miami, FL, USA, November 15-17, 2019, Revised Selected Papers. Lecture Notes in Computer Science 12029, Springer 2020, ISBN 978-3-030-46164-5 [contents]
2010 – 2019
- 2019
- [j77]Pavel Skums, Viachaslau Tsyvina, Alex Zelikovsky:
Inference of clonal selection in cancer populations using single-cell sequencing data. Bioinform. 35(14): i398-i407 (2019) - [j76]Zhipeng Cai, Pavel Skums, Alexander Zelikovsky:
Preface: 14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018). J. Comput. Biol. 26(8): 767-768 (2019) - [j75]Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 16(4): 1362-1363 (2019) - [c126]Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky:
Workshop on Computational Advances in Molecular Epidemiology. BCB 2019: 561 - [c125]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: 171-179 - [i11]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: e27885 (2019) - 2018
- [j74]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): 163-170 (2018) - [j73]Igor Mandric, Sergey Knyazev, Alex Zelikovsky:
Repeat-aware evaluation of scaffolding tools. Bioinform. 34(15): 2530-2537 (2018) - [j72]Seth Sims, Atkinson G. Longmire, David S. Campo, Sumathi Ramachandran, Magdalena Medrzycki, Lilia Ganova-Raeva, Yulin Lin, Amanda Sue, Hong Thai, Alexander Zelikovsky, Yury Khudyakov:
Automated quality control for a molecular surveillance system. BMC Bioinform. 19-S(11): 358:1-358:15 (2018) - [j71]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. 19-S(11): 360:1-360:10 (2018) - [j70]Zhipeng Cai, Pavel Skums, Alexander Zelikovsky:
Special IssuePreface: 13th International Symposium on BioinformaticsResearch and Applications (ISBRA 2017). J. Comput. Biol. 25(3): 251-252 (2018) - [c124]Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky:
ACM-BCB 2018 Computational Advances in Molecular Epidemiology (CAME) Chairs' Welcome. BCB 2018: 574 - [c123]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: 2:1-2:8 - [c122]Yubao Wu, Pavel Skums, Alex Zelikovsky, David Stiven Campo Rendon, Xueting Liao:
Predicting Opioid Epidemic by Using Twitter Data. ISBRA 2018: 314-318 - [p3]Andrew B. Kahng, Ion I. Mandoiu, Alexander Zelikovsky:
Practical Approximations of Steiner Trees in Uniform Orientation Metrics. Handbook of Approximation Algorithms and Metaheuristics (1) 2018: 657-669 - [p2]Ion I. Mandoiu, Alex Olshevsky, Alexander Zelikovsky:
QoS Multimedia Multicast Routing. Handbook of Approximation Algorithms and Metaheuristics (2) 2018 - [e7]Donghyun Kim, R. N. Uma, Alexander Zelikovsky:
Combinatorial Optimization and Applications - 12th International Conference, COCOA 2018, Atlanta, GA, USA, December 15-17, 2018, Proceedings. Lecture Notes in Computer Science 11346, Springer 2018, ISBN 978-3-030-04650-7 [contents] - 2017
- [j69]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): 3302-3304 (2017) - [j68]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): 244:1-244:6 (2017) - [j67]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): 558-570 (2017) - [j66]Robert W. Harrison, Ion I. Mandoiu, Alexander Zelikovsky:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 14(3): 576-577 (2017) - [c121]Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky:
CAME 2017: 6th Workshop on Computational Advances in Molecular Epidemiology. BCB 2017: 775 - [c120]Sunitha Basodi, Pelin Burcak Icer, Pavel Skums, Yury Khudyakov, Alexander Zelikovsky, Yi Pan:
Classification of HCV infections through sequence image normalization. ICCABS 2017: 1 - [c119]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: 1 - [c118]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: 1 - [c117]Igor Mandric, Sergey Knyazev, Cory Padilla, Frank Stewart, Ion I. Mandoiu, Alex Zelikovsky:
Metabolic Analysis of Metatranscriptomic Data from Planktonic Communities. ISBRA 2017: 396-402 - [c116]Alexander Artyomenko, Pelin B. Icer, Pavel Skums, Sumathi Ramachandran, Yury Khudyakov, Alex Zelikovsky:
Agent-Based in Silico Evolution of HCV Quasispecies. ISBRA 2017: 420-424 - [c115]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: 425-430 - 2016
- [j65]Zhipeng Cai, Alexander Zelikovsky:
Computing and Combinatorics. Algorithmica 76(4): 865-866 (2016) - [j64]Zhipeng Cai, Alexander Zelikovsky:
Special issue on Computing and Combinatorics Conference. Theor. Comput. Sci. 609: 515 (2016) - [c114]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: 80-92 - [c113]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: 164-175 - [e6]Anu G. Bourgeois, Pavel Skums, Xiang Wan, Alex Zelikovsky:
Bioinformatics Research and Applications - 12th International Symposium, ISBRA 2016, Minsk, Belarus, June 5-8, 2016, Proceedings. Lecture Notes in Computer Science 9683, Springer 2016, ISBN 978-3-319-38781-9 [contents] - 2015
- [j63]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): 682-690 (2015) - [j62]Igor Mandric, Alex Zelikovsky:
ScaffMatch: scaffolding algorithm based on maximum weight matching. Bioinform. 31(16): 2632-2638 (2015) - [j61]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): 695-704 (2015) - [c112]Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky:
2SNV: Quasispecies reconstruction from PacBio reads. ICCABS 2015: 1 - [c111]Ekaterina Nenastyeva, Alex Zelikovsky, Yurij Ionov, Ion I. Mandoiu:
Identification of cancer-specific motifs in mimotope profiles of serum antibody repertoire. ICCABS 2015: 1 - [c110]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: 1 - [c109]Ning Yu, Xuan Guo, Alexander Zelikovsky, Yi Pan:
GaussianCpG: A Gaussian model for detection of human CpG island. ICCABS 2015: 1 - [c108]Igor Mandric, Alex Zelikovsky:
ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching. RECOMB 2015: 222-223 - 2014
- [j60]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): 329-337 (2014) - [j59]James Lindsay, Hamed Salooti, Ion I. Mandoiu, Alexander Zelikovsky:
ILP-based maximum likelihood genome scaffolding. BMC Bioinform. 15(S-9): S9 (2014) - [c107]Alexander Artyomenko, Serghei Mangul, Nicholas C. Wu, Eleazar Eskin, Ren Sun, Alex Zelikovsky:
Reconstruction of influenza a virus variants from PacBio reads. ICCABS 2014: 1 - [c106]Adrian Caciula, Olga Glebova, Alexander Artyomenko, Serghei Mangul, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky:
Deterministic regression algorithm for transcriptome frequency estimation. ICCABS 2014: 1 - [c105]Igor Mandric, James Lindsay, Ion I. Mandoiu, Alex Zelikovsky:
SILP3: Maximum likelihood approach to scaffolding. ICCABS 2014: 1 - [c104]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: 1 - [c103]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: 1 - [e5]Zhipeng Cai, Alex Zelikovsky, Anu G. Bourgeois:
Computing and Combinatorics - 20th International Conference, COCOON 2014, Atlanta, GA, USA, August 4-6, 2014. Proceedings. Lecture Notes in Computer Science 8591, Springer 2014, ISBN 978-3-319-08782-5 [contents] - 2013
- [j58]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): S2 (2013) - [j57]Thamer Alsulaiman, Sushil K. Prasad, Alexander Zelikovsky:
Distributed Algorithms for TDMA Link Scheduling in Sensor Networks. Int. J. Netw. Comput. 3(1): 55-74 (2013) - [j56]Ion I. Mandoiu, Jianxin Wang, Alexander Zelikovsky:
Guest Editors' introduction to the special section on bioinformatics research and applications. IEEE ACM Trans. Comput. Biol. Bioinform. 10(6): 1345-1346 (2013) - [c102]Alexander Artyomenko, Nicholas Mancuso, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu:
kGEM: An EM-based algorithm for local reconstruction of viral quasispecies. ICCABS 2013: 1 - [c101]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: 1 - [c100]Gabriel Ilie, Alex Zelikovsky, Ion I. Mandoiu:
Reference assisted nucleic acid sequence reconstruction from mass spectrometry data. ICCABS 2013: 1 - [c99]Nicholas Mancuso, Alexander Artyomenko, Alex Zelikovsky, Pavel Skums, Ion I. Mandoiu:
Estimation of viral population structure from amplicon-based reads. ICCABS 2013: 1 - [c98]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: 1 - [c97]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: 1 - [c96]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: 149-160 - 2012
- [j55]Gruia Calinescu, Cristina G. Fernandes, Hemanshu Kaul, Alexander Zelikovsky:
Maximum Series-Parallel Subgraph. Algorithmica 63(1-2): 137-157 (2012) - [j54]Jianer Chen, Ion I. Mandoiu, Raj Sunderraman, Jianxin Wang, Alexander Zelikovsky:
Guest Editors' Introduction. BMC Bioinform. 13(S-10): S1 (2012) - [j53]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): S6 (2012) - [j52]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): A11 (2012) - [j51]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): 237-249 (2012) - [j50]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): 251-261 (2012) - [j49]Jianer Chen, Alexander Zelikovsky:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 9(4): 1002-1003 (2012) - [c95]James Lindsay, Hamed Salooti, Alexander Zelikovsky, Ion I. Mandoiu:
Scalable genome scaffolding using integer linear programming. BCB 2012: 377-383 - [c94]James Lindsay, Ion I. Mandoiu, Hamed Salooti, Alexander Zelikovsky:
Poster: Accurate scaffolding of large genomes using integer programming and Non-Serial Dynamic Programming. ICCABS 2012: 1 - [c93]Nicholas Mancuso, Bassam Tork, Pavel Skums, Lilia Ganova-Raeva, Ion I. Mandoiu, Alexander Zelikovsky:
Workshop: A maximum likelihood method for quasispecies spectrum assembly. ICCABS 2012: 1 - [c92]Serghei Mangul, Adrian Caciula, Ion I. Mandoiu, Alexander Zelikovsky:
Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution. ICCABS 2012: 1 - [c91]Rachel J. O'Neill, Ion I. Mandoiu, Mazhar I. Khan, Craig Obergfell, Hongjun Wang, Andrew Bligh, Bassam Tork, Nicholas Mancuso, Alexander Zelikovsky:
Workshop: Bioinformatics methods for reconstruction of Infectious Bronchitis Virus quasispecies from next generation sequencing data. ICCABS 2012: 1 - [c90]Thamer Alsulaiman, Sushil K. Prasad, Alexander Zelikovsky:
Distributed Algorithms for TDMA Link Scheduling in Sensor Networks. IPDPS Workshops 2012: 839-847 - 2011
- [j48]