Serghei Mangul

Title(s)Assistant Professor
Address1540 Alcazar St., CHP 236D
Health Sciences Campus
Los Angeles CA 90089
Phone+1 323 442 0043
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction. Nucleic Acids Res. 2021 Jul 02. Knyazev S, Tsyvina V, Shankar A, Melnyk A, Artyomenko A, Malygina T, Porozov YB, Campbell EM, Switzer WM, Skums P, Mangul S, Zelikovsky A. PMID: 34214168.
      View in: PubMed   Mentions:    Fields:    
    2. Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19. J Clin Invest. 2021 May 27. Povysil G, Butler-Laporte G, Shang N, Wang C, Khan A, Alaamery M, Nakanishi T, Zhou S, Forgetta V, Eveleigh RJM, Bourgey M, Aziz N, Jones SJ, Knoppers B, Scherer SW, Strug LJ, Lepage P, Ragoussis J, Bourque G, Alghamdi J, Aljawini N, Albesher N, Al-Afghani HM, Alghamdi B, Almutair MS, Mahmoud ES, Abu-Safieh L, El Bardisy H, Al Harthi FS, Alshareef A, Suliman BA, Alqahtani SA, Almalik A, Alrashed MM, Massadeh S, Mooser V, Lathrop M, Fawzy M, Arabi YM, Mbarek H, Saad C, Al-Muftah W, Jung J, Mangul S, Badji R, Thani AA, Ismail SI, Gharavi AG, Abedalthagafi MS, Richards JB, Goldstein DB, Kiryluk K. PMID: 34043590.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    3. Detection of viral gene expression in risk-stratified biopsies reveals no active HPV in cutaneous squamous cell carcinoma. Exp Dermatol. 2021 May 25. Vandiver AR, Thomas BJ, Karimzada M, Knowles BC, Botten GA, Spreafico R, Rotman JN, Gharavi NM, Chesnut C, Wesel K, Mangul S, Soriano T, Scumpia PO. PMID: 34036652.
      View in: PubMed   Mentions:    Fields:    
    4. Diversity in immunogenomics: the value and the challenge. Nat Methods. 2021 May 17. Peng K, Safonova Y, Shugay M, Popejoy AB, Rodriguez OL, Breden F, Brodin P, Burkhardt AM, Bustamante C, Cao-Lormeau VM, Corcoran MM, Duffy D, Fuentes-Guajardo M, Fujita R, Greiff V, Jönsson VD, Liu X, Quintana-Murci L, Rossetti M, Xie J, Yaari G, Zhang W, Abedalthagafi MS, Adekoya KO, Ahmed RA, Chang WC, Gray C, Nakamura Y, Lees WD, Khatri P, Alachkar H, Scheepers C, Watson CT, Karlsson Hedestam GB, Mangul S. PMID: 34002093.
      View in: PubMed   Mentions: 1     Fields:    
    5. Unlocking capacities of viral genomics for the COVID-19 pandemic response. ArXiv. 2021 Apr 28. 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, Ladner J, Lam TT, Wu N, Zelikovsky A, Knight R, Crandall K, Mangul S. PMID: 33948451.
      View in: PubMed   Mentions:
    6. Improving the completeness of public metadata accompanying omics studies. Genome Biol. 2021 Apr 15; 22(1):106. Rajesh A, Chang Y, Abedalthagafi MS, Wong-Beringer A, Love MI, Mangul S. PMID: 33858487.
      View in: PubMed   Mentions:    Fields:    
    7. The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data. Gigascience. 2021 Feb 16; 10(2). Nadel BB, Lopez D, Montoya DJ, Ma F, Waddel H, Khan MM, Mangul S, Pellegrini M. PMID: 33590863.
      View in: PubMed   Mentions: 2     Fields:    
    8. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through analysis of Viral Genomics and Structure. ArXiv. 2021 Feb 01. Rando HM, MacLean AL, Lee AJ, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, McGowan LD, Guebila MB, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Sun Y, Mai D, Brueffer C, Byrd JB, Wang J, Lordan R, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, Consortium CR, Gitter A, Greene CS. PMID: 33594340.
      View in: PubMed   Mentions:
    9. PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom. Front Microbiol. 2020; 11:584699. Mitchell K, Ronas J, Dao C, Freise AC, Mangul S, Shapiro C, Moberg Parker J. PMID: 33123113.
      View in: PubMed   Mentions:
    10. Corrigendum to: Recommendations to enhance rigor and reproducibility in biomedical research. Gigascience. 2020 09 17; 9(9). Brito JJ, Li J, Moore JH, Greene CS, Nogoy NA, Garmire LX, Mangul S. PMID: 32940333.
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    11. Cell type-specific genetic regulation of gene expression across human tissues. Science. 2020 09 11; 369(6509). Kim-Hellmuth S, Aguet F, Oliva M, Muñoz-Aguirre M, Kasela S, Wucher V, Castel SE, Hamel AR, Viñuela A, Roberts AL, Mangul S, Wen X, Wang G, Barbeira AN, Garrido-Martín D, Nadel BB, Zou Y, Bonazzola R, Quan J, Brown A, Martinez-Perez A, Soria JM, GTEx Consortium , Getz G, Dermitzakis ET, Small KS, Stephens M, Xi HS, Im HK, Guigó R, Segrè AV, Stranger BE, Ardlie KG, Lappalainen T. PMID: 32913075.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    12. Metalign: efficient alignment-based metagenomic profiling via containment min hash. Genome Biol. 2020 09 10; 21(1):242. LaPierre N, Alser M, Eskin E, Koslicki D, Mangul S. PMID: 32912225.
      View in: PubMed   Mentions: 2     Fields:    
    13. Author Correction: Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing. Nat Commun. 2020 09 04; 11(1):4499. 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, Ansel KM, Eskin E, Mangul S. PMID: 32887888.
      View in: PubMed   Mentions:    Fields:    
    14. Correction to: Improving the usability and comprehensiveness of microbial databases. BMC Biol. 2020 07 28; 18(1):92. Loeffler C, Karlsberg A, Martin LS, Eskin E, Koslicki D, Mangul S. PMID: 32723395.
      View in: PubMed   Mentions:    Fields:    
    15. Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing. Nat Commun. 2020 06 19; 11(1):3126. 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, Ansel KM, Eskin E, Mangul S. PMID: 32561710.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    16. Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer. Cell. 2020 06 25; 181(7):1612-1625.e13. Oh DY, Kwek SS, Raju SS, Li T, McCarthy E, Chow E, Aran D, Ilano A, Pai CS, Rancan C, Allaire K, Burra A, Sun Y, Spitzer MH, Mangul S, Porten S, Meng MV, Friedlander TW, Ye CJ, Fong L. PMID: 32497499.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    17. Recommendations to enhance rigor and reproducibility in biomedical research. Gigascience. 2020 06 01; 9(6). Brito JJ, Li J, Moore JH, Greene CS, Nogoy NA, Garmire LX, Mangul S. PMID: 32479592.
      View in: PubMed   Mentions: 8     Fields:    
    18. Improving the usability and comprehensiveness of microbial databases. BMC Biol. 2020 04 07; 18(1):37. Loeffler C, Karlsberg A, Martin LS, Eskin E, Koslicki D, Mangul S. PMID: 32264902.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    19. Benchmarking of computational error-correction methods for next-generation sequencing data. Genome Biol. 2020 03 17; 21(1):71. 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, Littman E, Shabani T, Enik G, Yao D, Sun R, Schroeder J, Eskin E, Zelikovsky A, Skums P, Pop M, Mangul S. PMID: 32183840.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    20. Telescope: an interactive tool for managing large-scale analysis from mobile devices. Gigascience. 2020 01 01; 9(1). Brito JJ, Mosqueiro T, Rotman J, Xue V, Chapski DJ, la Hoz J, Matias P, Martin LS, Zelikovsky A, Pellegrini M, Mangul S. PMID: 31972019.
      View in: PubMed   Mentions:    Fields:    
    21. Interpreting and integrating big data in the life sciences. Emerg Top Life Sci. 2019 Aug 16; 3(4):335-341. Mangul S. PMID: 33523204.
      View in: PubMed   Mentions:
    22. Transcriptional profiling of single fiber cells in a transgenic paradigm of an inherited childhood cataract reveals absence of molecular heterogeneity. J Biol Chem. 2019 09 13; 294(37):13530-13544. Bhat SP, Gangalum RK, Kim D, Mangul S, Kashyap RK, Zhou X, Elashoff D. PMID: 31243103.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    23. Challenges and recommendations to improve the installability and archival stability of omics computational tools. PLoS Biol. 2019 06; 17(6):e3000333. 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, Eskin E, Blekhman R. PMID: 31220077.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    24. MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples. BMC Genomics. 2019 Jun 06; 20(Suppl 5):423. LaPierre N, Mangul S, Alser M, Mandric I, Wu NC, Koslicki D, Eskin E. PMID: 31167634.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    25. Systematic benchmarking of omics computational tools. Nat Commun. 2019 03 27; 10(1):1393. Mangul S, Martin LS, Hill BL, Lam AK, Distler MG, Zelikovsky A, Eskin E, Flint J. PMID: 30918265.
      View in: PubMed   Mentions: 23     Fields:    Translation:Humans
    26. How bioinformatics and open data can boost basic science in countries and universities with limited resources. Nat Biotechnol. 2019 03; 37(3):324-326. Mangul S, Martin LS, Langmead B, Sanchez-Galan JE, Toma I, Hormozdiari F, Pevzner P, Eskin E. PMID: 30833765.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    27. Improving the usability and archival stability of bioinformatics software. Genome Biol. 2019 02 27; 20(1):47. Mangul S, Martin LS, Eskin E, Blekhman R. PMID: 30813962.
      View in: PubMed   Mentions: 14     Fields:    
    28. Spatial Analysis of Single Fiber Cells of the Developing Ocular Lens Reveals Regulated Heterogeneity of Gene Expression. iScience. 2018 Dec 21; 10:66-79. Gangalum RK, Kim D, Kashyap RK, Mangul S, Zhou X, Elashoff D, Bhat SP. PMID: 30508719.
      View in: PubMed   Mentions:
    29. A Comprehensive Map of Genetic Variation in the World's Largest Ethnic Group-Han Chinese. Mol Biol Evol. 2018 11 01; 35(11):2736-2750. Chiang CWK, Mangul S, Robles C, Sankararaman S. PMID: 30169787.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimals
    30. Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia. Transl Psychiatry. 2018 05 10; 8(1):96. Olde Loohuis LM, Mangul S, Ori APS, Jospin G, Koslicki D, Yang HT, Wu T, Boks MP, Lomen-Hoerth C, Wiedau-Pazos M, Cantor RM, de Vos WM, Kahn RS, Eskin E, Ophoff RA. PMID: 29743478.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    31. Involving undergraduates in genomics research to narrow the education-research gap. Nat Biotechnol. 2018 04 05; 36(4):369-371. Mangul S, Martin LS, Eskin E. PMID: 29621227.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    32. ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues. Genome Biol. 2018 02 15; 19(1):36. 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, Ophoff RA, Santana JR, Levanon EY, Woodruff PG, Burchard E, Seibold MA, Shifman S, Eskin E, Zaitlen N. PMID: 29548336.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    33. Addressing the Digital Divide in Contemporary Biology: Lessons from Teaching UNIX. Trends Biotechnol. 2017 10; 35(10):901-903. Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E. PMID: 28720283.
      View in: PubMed   Mentions: 6     Fields:    
    34. HapIso: An Accurate Method for the Haplotype- Specific Isoforms Reconstruction From Long Single-Molecule Reads. IEEE Trans Nanobioscience. 2017 03; 16(2):108-115. Mangul S, Yang TH, Hormozdiari F, Dainis AM, Tseng E, Ashley EA, Zelikovsky A, Eskin E. PMID: 28328508.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    35. Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants. J Comput Biol. 2017 Jun; 24(6):558-570. Artyomenko A, Wu NC, Mangul S, Eskin E, Sun R, Zelikovsky A. PMID: 27901586.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    36. Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data. Genetics. 2016 11; 204(3):1057-1064. Kang EY, Martin LJ, Mangul S, Isvilanonda W, Zou J, Ben-David E, Han B, Lusis AJ, Shifman S, Eskin E. PMID: 27765809.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    37. CRISPR-Mediated VHL Knockout Generates an Improved Model for Metastatic Renal Cell Carcinoma. Sci Rep. 2016 06 30; 6:29032. Schokrpur S, Hu J, Moughon DL, Liu P, Lin LC, Hermann K, Mangul S, Guan W, Pellegrini M, Xu H, Wu L. PMID: 27358011.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    38. Transcriptome assembly and quantification from Ion Torrent RNA-Seq data. BMC Genomics. 2014; 15 Suppl 5:S7. Mangul S, Caciula A, Al Seesi S, Brinza D, M?ndoiu I, Zelikovsky A. PMID: 25082147.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    39. Accurate viral population assembly from ultra-deep sequencing data. Bioinformatics. 2014 Jun 15; 30(12):i329-37. Mangul S, Wu NC, Mancuso N, Zelikovsky A, Sun R, Eskin E. PMID: 24932001.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    40. Inferring viral quasispecies spectra from 454 pyrosequencing reads. BMC Bioinformatics. 2011; 12 Suppl 6:S1. Astrovskaya I, Tork B, Mangul S, Westbrooks K, Mandoiu I, Balfe P, Zelikovsky A. PMID: 21989211.
      View in: PubMed   Mentions: 40     Fields:    Translation:HumansCells
    41. Estimation of alternative splicing isoform frequencies from RNA-Seq data. Algorithms Mol Biol. 2011 Apr 19; 6(1):9. Nicolae M, Mangul S, Mandoiu II, Zelikovsky A. PMID: 21504602.
      View in: PubMed   Mentions:
    42. Improved transcriptome quantification and reconstruction from RNA-Seq reads using partial annotations. In Silico Biol. 2011-2012; 11(5-6):251-61. Mangul S, Caciula A, Glebova O, Mandoiu I, Zelikovsky A. PMID: 23202426.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
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