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Serghei Mangul, Ph.D. - Publications

Affiliations: 
2012 Computer Science Georgia State University, Atlanta, GA, United States 
Area:
Computer Science, Bioinformatics, Epidemiology
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41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Sarwal V, Lee S, Yang J, Sankararaman S, Chaisson M, Eskin E, Mangul S. VISTA: an integrated framework for structural variant discovery. Briefings in Bioinformatics. 25. PMID 39297879 DOI: 10.1093/bib/bbae462  0.32
2024 Boltz TA, Chu BB, Liao C, Sealock JM, Ye R, Majara L, Fu JM, Service S, Zhan L, Medland SE, Chapman SB, Rubinacci S, DeFelice M, Grimsby JL, Abebe T, ... ... Mangul S, et al. A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner. Biorxiv : the Preprint Server For Biology. PMID 39282356 DOI: 10.1101/2024.09.06.611689  0.313
2024 Mohebbi F, Zelikovsky A, Mangul S, Chowell G, Skums P. Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks. Nature Communications. 15: 2838. PMID 38565543 DOI: 10.1038/s41467-024-47304-6  0.541
2024 Yu D, Ayyala R, Sadek SH, Chittampalli L, Farooq H, Jung J, Nahid AA, Boldirev G, Jung M, Park S, Nguyen A, Zelikovsky A, Mancuso N, Joo JWJ, Thompson RF, ... ... Mangul S, et al. A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data. Biorxiv : the Preprint Server For Biology. PMID 38293199 DOI: 10.1101/2023.05.22.541750  0.539
2023 Peng K, Nowicki TS, Campbell K, Vahed M, Peng D, Meng Y, Nagareddy A, Huang YN, Karlsberg A, Miller Z, Brito J, Nadel B, Pak VM, Abedalthagafi MS, Burkhardt AM, ... ... Mangul S, et al. Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing. Briefings in Bioinformatics. PMID 37291798 DOI: 10.1093/bib/bbad220  0.349
2023 Deshpande D, Chhugani K, Chang Y, Karlsberg A, Loeffler C, Zhang J, Muszyńska A, Munteanu V, Yang H, Rotman J, Tao L, Balliu B, Tseng E, Eskin E, Zhao F, ... ... Mangul S, et al. RNA-seq data science: From raw data to effective interpretation. Frontiers in Genetics. 14: 997383. PMID 36999049 DOI: 10.3389/fgene.2023.997383  0.392
2022 Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, ... ... Mangul S, et al. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nature Methods. 19: 429-440. PMID 35396482 DOI: 10.1038/s41592-022-01431-4  0.311
2022 Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Baykal PI, Comarova Z, Lu A, Porozov Y, Vasylyeva TI, Wertheim JO, Tierney BT, Chiu CY, ... ... Mangul S, et al. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nature Methods. 19: 374-380. PMID 35396471 DOI: 10.1038/s41592-022-01444-z  0.498
2021 Alser M, Rotman J, Deshpande D, Taraszka K, Shi H, Baykal PI, Yang HT, Xue V, Knyazev S, Singer BD, Balliu B, Koslicki D, Skums P, Zelikovsky A, Alkan C, ... ... Mangul S, et al. Technology dictates algorithms: recent developments in read alignment. Genome Biology. 22: 249. PMID 34446078 DOI: 10.1186/s13059-021-02443-7  0.554
2021 Knyazev S, Tsyvina V, Shankar A, Melnyk A, Artyomenko A, Malygina T, Porozov YB, Campbell EM, Switzer WM, Skums P, Mangul S, Zelikovsky A. Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction. Nucleic Acids Research. PMID 34214168 DOI: 10.1093/nar/gkab576  0.595
2021 Knyazev S, Chhugani K, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Comarova Z, Lu A, Sarwal V, Porozov Y, Wu A, Abedalthagafi M, Nagaraj S, Smith A, Skums P, ... ... Mangul S, et al. Unlocking capacities of viral genomics for the COVID-19 pandemic response. Arxiv. PMID 33948451  0.549
2020 Mandric I, Rotman J, Yang HT, Strauli N, Montoya DJ, Van Der Wey W, Ronas JR, Statz B, Yao D, Petrova V, Zelikovsky A, Spreafico R, Shifman S, Zaitlen N, Rossetti M, ... ... Mangul S, et al. Author Correction: Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing. Nature Communications. 11: 4499. PMID 32887888 DOI: 10.1038/S41467-020-18509-2  0.589
2020 Mandric I, Rotman J, Yang HT, Strauli N, Montoya DJ, Van Der Wey W, Ronas JR, Statz B, Yao D, Petrova V, Zelikovsky A, Spreafico R, Shifman S, Zaitlen N, Rossetti M, ... ... Mangul S, et al. Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing. Nature Communications. 11: 3126. PMID 32561710 DOI: 10.1038/S41467-020-16857-7  0.563
2020 Mitchell K, Brito JJ, Mandric I, Wu Q, Knyazev S, Chang S, Martin LS, Karlsberg A, Gerasimov E, Littman R, Hill BL, Wu NC, Yang HT, Hsieh K, Chen L, ... ... Mangul S, et al. Benchmarking of computational error-correction methods for next-generation sequencing data. Genome Biology. 21: 71. PMID 32183840 DOI: 10.1186/S13059-020-01988-3  0.581
2020 Brito JJ, Mosqueiro T, Rotman J, Xue V, Chapski DJ, la Hoz J, Matias P, Martin LS, Zelikovsky A, Pellegrini M, Mangul S. Telescope: an interactive tool for managing large-scale analysis from mobile devices. Gigascience. 9. PMID 31972019 DOI: 10.1093/Gigascience/Giz163  0.462
2019 Mangul S, Mosqueiro T, Abdill RJ, Duong D, Mitchell K, Sarwal V, Hill B, Brito J, Littman RJ, Statz B, Lam AK, Dayama G, Grieneisen L, Martin LS, Flint J, et al. Challenges and recommendations to improve the installability and archival stability of omics computational tools. Plos Biology. 17: e3000333. PMID 31220077 DOI: 10.1371/Journal.Pbio.3000333  0.307
2019 LaPierre N, Mangul S, Alser M, Mandric I, Wu NC, Koslicki D, Eskin E. MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples. Bmc Genomics. 20: 423. PMID 31167634 DOI: 10.1186/S12864-019-5699-9  0.317
2019 Mangul S, Martin LS, Hill BL, Lam AK, Distler MG, Zelikovsky A, Eskin E, Flint J. Systematic benchmarking of omics computational tools. Nature Communications. 10: 1393. PMID 30918265 DOI: 10.1038/S41467-019-09406-4  0.546
2018 Mangul S, Martin LS, Eskin E. Involving undergraduates in genomics research to narrow the education-research gap. Nature Biotechnology. 36: 369-371. PMID 29621227 DOI: 10.1038/Nbt.4113  0.301
2018 Mangul S, Yang HT, Strauli N, Gruhl F, Porath HT, Hsieh K, Chen L, Daley T, Christenson S, Wesolowska-Andersen A, Spreafico R, Rios C, Eng C, Smith AD, Hernandez RD, et al. ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. Genome Biology. 19: 36. PMID 29548336 DOI: 10.1186/S13059-018-1403-7  0.503
2017 Mangul S, Yang HT, Hormozdiari F, Dainis A, Tseng E, Ashley EA, Zelikovsky A, Eskin E. HapIso : An Accurate Method for the Haplotype-Specific Isoforms Reconstruction from Long Single-Molecule Reads. Ieee Transactions On Nanobioscience. PMID 28328508 DOI: 10.1109/Tnb.2017.2675981  0.628
2016 Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, Zelikovsky A. Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. PMID 27901586 DOI: 10.1089/Cmb.2016.0146  0.642
2016 Kang EY, Martin L, Mangul S, Isvilanonda W, Zou J, Ben-David E, Han B, Lusis AJ, Shifman S, Eskin E. Discovering SNPs Regulating Human Gene Expression Using Allele Specific Expression from RNA-Seq Data. Genetics. PMID 27765809 DOI: 10.1534/Genetics.115.177246  0.391
2016 Mangul S, Taegyun Yang H, Hormozdiari F, Tseng E, Zelikovsky A, Eskin E. HapIso: An accurate method for the haplotype-specific isoforms reconstruction from long single-molecule reads Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9683: 80-92. DOI: 10.1007/978-3-319-38782-6_7  0.576
2016 Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, Zelikovsky A. Long single-molecule reads can resolve the complexity of the influenza virus composed of rare, closely related mutant variants Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9649: 164-175. DOI: 10.1007/978-3-319-31957-5_12  0.615
2015 Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, Zelikovsky A. 2SNV: Quasispecies reconstruction from PacBio reads 2015 Ieee 5th International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2015. DOI: 10.1109/ICCABS.2015.7344730  0.605
2014 Mangul S, Caciula A, Al Seesi S, Brinza D, Mӑndoiu I, Zelikovsky A. Transcriptome assembly and quantification from Ion Torrent RNA-Seq data. Bmc Genomics. 15: S7. PMID 25082147 DOI: 10.1186/1471-2164-15-S5-S7  0.76
2014 Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E. Accurate viral population assembly from ultra-deep sequencing data. Bioinformatics (Oxford, England). 30: i329-37. PMID 24932001 DOI: 10.1093/Bioinformatics/Btu295  0.668
2014 Caciula A, Glebova O, Artyomenko A, Mangul S, Lindsay J, Məndoiu II, Zelikovsky A. Deterministic regression algorithm for transcriptome frequency estimation 2014 Ieee 4th International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2014. DOI: 10.1109/ICCABS.2014.6863946  0.572
2014 Artyomenko A, Mangul S, Wu NC, Eskin E, Sun R, Zelikovsky A. Reconstruction of influenza a virus variants from PacBio reads 2014 Ieee 4th International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2014. DOI: 10.1109/ICCABS.2014.6863935  0.569
2014 Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E. VGA: A method for viral quasispecies assembly from ultra-deep sequencing data 2014 Ieee 4th International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2014. DOI: 10.1109/ICCABS.2014.6863932  0.626
2013 Caciula A, Zelikovsky A, Mangul S, Lindsay J, Mandoiu I. Monte-Carlo Regression algorithm for isoform frequency estimation from RNA-Seq data 2013 Ieee 3rd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2013. DOI: 10.1109/ICCABS.2013.6629228  0.588
2013 Mangul S, Caciula A, Seesi SA, Brinza D, Banday AR, Kanadia R, Mandoiu I, Zelikovsky A. Flexible approach for novel transcript reconstruction from RNA-seq data using maximum likelihood integer programming 5th International Conference On Bioinformatics and Computational Biology 2013, Bicob 2013. 25-33.  0.707
2012 Mangul S, Caciula A, Brinza D, Mandoiu II, Zelikovsky A. TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads Bmc Bioinformatics. 13. DOI: 10.1186/1471-2105-13-S18-A11  0.775
2012 Mangul S, Caciula A, Al Seesi S, Brinza D, Banday AR, Kanadia R. An Integer Programming approach to novel transcript reconstruction from paired-end RNA-Seq reads 2012 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2012. 369-376. DOI: 10.1145/2382936.2382983  0.655
2012 Mangul S, Caciula A, Mandoiu I, Zelikovsky A. Workshop: Novel transcript reconstruction from paired-end RNA-Seq reads using fragment length distribution 2012 Ieee 2nd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2012. DOI: 10.1109/ICCABS.2012.6182673  0.674
2011 Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A. Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations. In Silico Biology. 11: 251-61. PMID 23202426 DOI: 10.3233/Isb-2012-0459  0.689
2011 Astrovskaya I, Tork B, Mangul S, Westbrooks K, Măndoiu I, Balfe P, Zelikovsky A. Inferring viral quasispecies spectra from 454 pyrosequencing reads. Bmc Bioinformatics. 12: S1. PMID 21989211 DOI: 10.1186/1471-2105-12-S6-S1  0.763
2011 Nicolae M, Mangul S, Măndoiu II, Zelikovsky A. Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms For Molecular Biology : Amb. 6: 9. PMID 21504602 DOI: 10.1186/1748-7188-6-9  0.672
2011 Mangul S, Caciula A, Mandoiu I, Zelikovsky A. RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes 2011 Ieee International Conference On Bioinformatics and Biomedicine Workshops, Bibmw 2011. 118-123. DOI: 10.1109/BIBMW.2011.6112363  0.649
2011 Mangul S, Astrovskaya I, Nicolae M, Tork B, Mandoiu I, Zelikovsky A. Maximum likelihood estimation of incomplete genomic spectrum from HTS data Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6833: 213-224. DOI: 10.1007/978-3-642-23038-7_19  0.77
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