Serghei Mangul

Title(s)Assistant Professor
SchoolUSC School of Pharmacy
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. Pioneering Computational Culture Within Pharmacy Schools by Empowering Students With Data Science and Bioinformatics Skills. Am J Pharm Educ. 2024 Dec 12; 101341. Ronkowski C, Deshpande D, Sharma N, Vahed M, Patel YM, Gukasyan HJ, Wu M, Peng K, Church TD, Kim RE, Mirzaian E, Padula WV, Tomaszewski D, Ng TMH, Wong-Beringer A, Zaro J, Qato DM, Davies DL, Papadopoulos V, Mangul S. PMID: 39674347.
      View in: PubMed   Mentions:    Fields:    
    2. CAMP: A modular metagenomics analysis system for integrated multi-step data exploration. bioRxiv. 2024 Sep 14. Mak L, Tierney B, Ronkowski C, Toscan RB, Turhan B, Toomey M, Martinez JSA, Fu C, Lucaci AG, Solano AHB, Setubal JC, Henriksen JR, Zimmerman S, Kopbayeva M, Noyvert A, Iwan Z, Kar S, Nakazawa N, Meleshko D, Horyslavets D, Kantsypa V, Frolova A, Kahles A, Danko D, Elhaik E, Labaj P, Mangul S, International MetaSUB Consortium, Mason CE, Hajirasouliha I. PMID: 37066359; PMCID: PMC10104186.
      View in: PubMed   Mentions:
    3. A blended genome and exome sequencing method captures genetic variation in an unbiased, high-quality, and cost-effective manner. bioRxiv. 2024 Sep 08. 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, Alemayehu M, Ashaba FK, Atkinson EG, Bigdeli T, Bradway AB, Brand H, Chibnik LB, Fekadu A, Gatzen M, Gelaye B, Gichuru S, Gildea ML, Hill TC, Huang H, Hubbard KM, Injera WE, James R, Joloba M, Kachulis C, Kalmbach PR, Kamulegeya R, Kigen G, Kim S, Koen N, Kwobah EK, Kyebuzibwa J, Lee S, Lennon NJ, Lind PA, Lopera-Maya EA, Makale J, Mangul S, McMahon J, Mowlem P, Musinguzi H, Mwema RM, Nakasujja N, Newman CP, Nkambule LL, O'Neil CR, Olivares AM, Olsen CM, Ongeri L, Parsa SJ, Pretorius A, Ramesar R, Reagan FL, Sabatti C, Schneider JA, Shiferaw W, Stevenson A, Stricker E, Stroud RE, Tang J, Whiteman D, Yohannes MT, Yu M, Yuan K, NeuroGAP-Psychosis, Akena D, Atwoli L, Kariuki SM, Koenen KC, Newton CRJC, Stein DJ, Teferra S, Zingela Z, Pato CN, Pato MT, Lopez-Jaramillo C, Freimer N, Ophoff RA, Olde Loohuis LM, Talkowski ME, Neale BM, Howrigan DP, Martin AR. PMID: 39282356; PMCID: PMC11398523.
      View in: PubMed   Mentions:
    4. The evolution of computational research in a data-centric world. Cell. 2024 Aug 22; 187(17):4449-4457. Deshpande D, Chhugani K, Ramesh T, Pellegrini M, Shiffman S, Abedalthagafi MS, Alqahtani S, Ye J, Liu XS, Leek JT, Brazma A, Ophoff RA, Rao G, Butte AJ, Moore JH, Katritch V, Mangul S. PMID: 39178828.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    5. Genomic reproducibility in the bioinformatics era. Genome Biol. 2024 Aug 09; 25(1):213. Baykal PI, Labaj PP, Markowetz F, Schriml LM, Stekhoven DJ, Mangul S, Beerenwinkel N. PMID: 39123217; PMCID: PMC11312195.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    6. VISTA: an integrated framework for structural variant discovery. Brief Bioinform. 2024 Jul 25; 25(5). Sarwal V, Lee S, Yang J, Sankararaman S, Chaisson M, Eskin E, Mangul S. PMID: 39297879; PMCID: PMC11411772.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    7. Analytical code sharing practices in biomedical research. PeerJ Comput Sci. 2024; 10:e2066. Sharma NK, Ayyala R, Deshpande D, Patel Y, Munteanu V, Ciorba D, Bostan V, Fiscutean A, Vahed M, Sarkar A, Guo R, Moore A, Darci-Maher N, Nogoy N, Abedalthagafi M, Mangul S. PMID: 38983240; PMCID: PMC11232620.
      View in: PubMed   Mentions: 1  
    8. Estimating Enzyme Expression and Metabolic Pathway Activity in Borreliella-Infected and Uninfected Mice. J Comput Biol. 2024 Jun 27. Rondel FM, Farooq H, Hosseini R, Juyal A, Knyazev S, Mangul S, Rogovskyy AS, Zelikovsky A. PMID: 38934087.
      View in: PubMed   Mentions: 1     Fields:    
    9. The DNA methylation landscape across the TCR loci in patients with acute myeloid leukemia. Int Immunopharmacol. 2024 Sep 10; 138:112376. Pospiech M, Beckford J, Kumar AMS, Tamizharasan M, Brito J, Liang G, Mangul S, Alachkar H. PMID: 38917523.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    10. Early detection of emerging viral variants through analysis of community structure of coordinated substitution networks. Nat Commun. 2024 Apr 02; 15(1):2838. Mohebbi F, Zelikovsky A, Mangul S, Chowell G, Skums P. PMID: 38565543; PMCID: PMC10987511.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    11. Packaging and containerization of computational methods. Nat Protoc. 2024 Sep; 19(9):2529-2539. Alser M, Lawlor B, Abdill RJ, Waymost S, Ayyala R, Rajkumar N, LaPierre N, Brito J, Ribeiro-Dos-Santos AM, Almadhoun N, Sarwal V, Firtina C, Osinski T, Eskin E, Hu Q, Strong D, Kim BBD, Abedalthagafi MS, Mutlu O, Mangul S. PMID: 38565959.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    12. The knowns and unknowns of long COVID-19: from mechanisms to therapeutical approaches. Front Immunol. 2024; 15:1344086. Gheorghita R, Soldanescu I, Lobiuc A, Caliman Sturdza OA, Filip R, Constantinescu-Bercu A, Dimian M, Mangul S, Covasa M. PMID: 38500880; PMCID: PMC10944866.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    13. Climate warming, environmental degradation and pollution as drivers of antibiotic resistance. Environ Pollut. 2024 Apr 01; 346:123649. Rzymski P, Gwenzi W, Poniedzialek B, Mangul S, Fal A. PMID: 38402936.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCellsPHPublic Health
    14. Large-scale integrative analysis of juvenile idiopathic arthritis for new insight into its pathogenesis. Arthritis Res Ther. 2024 02 10; 26(1):47. Kim D, Song J, Mancuso N, Mangul S, Jung J, Jang W. PMID: 38336809; PMCID: PMC10858498.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    15. A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data. bioRxiv. 2024 Jan 16. 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, Alachkar H, Mangul S. PMID: 38293199; PMCID: PMC10827116.
      View in: PubMed   Mentions:
    16. Fasting-Mimicking Diet Inhibits Autophagy and Synergizes with Chemotherapy to Promote T-Cell-Dependent Leukemia-Free Survival. Cancers (Basel). 2023 Dec 16; 15(24). Buono R, Tucci J, Cutri R, Guidi N, Mangul S, Raucci F, Pellegrini M, Mittelman SD, Longo VD. PMID: 38136414; PMCID: PMC10741737.
      View in: PubMed   Mentions: 1  
    17. Whole blood transcriptomics identifies subclasses of pediatric septic shock. Crit Care. 2023 12 08; 27(1):486. Yang JO, Zinter MS, Pellegrini M, Wong MY, Gala K, Markovic D, Nadel B, Peng K, Do N, Mangul S, Nadkarni VM, Karlsberg A, Deshpande D, Butte MJ, Asaro L, Agus M, Sapru A, Study Site Investigators for CAF-PINT. PMID: 38066613; PMCID: PMC10709863.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    18. Response to 'comment on rigorous benchmarking of T cell receptor repertoire profiling methods for cancer RNA sequencing' by Davydov A.N.; Bolotin D.A.; Poslavsky S. V. and Chudakov D.M. Brief Bioinform. 2023 09 22; 24(6). Huang YN, Vahed M, Peng K, Alachkar H, Mangul S. PMID: 37824736; PMCID: PMC10569746.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    19. The Genomic Landscape of Colorectal Cancer in the Saudi Arabian Population Using a Comprehensive Genomic Panel. Diagnostics (Basel). 2023 Sep 19; 13(18). Alsolme E, Alqahtani S, Fageeh M, Barakeh D, Sharma NK, Mangul S, Robinson HA, Fathaddin A, Hauser CAE, Abedalthagafi M. PMID: 37761360; PMCID: PMC10527739.
      View in: PubMed   Mentions:
    20. Whole Blood Transcriptomics Identifies Subclasses of Pediatric Septic Shock. Res Sq. 2023 Aug 28. Yang JO, Zinter MS, Pellegrini M, Wong MY, Gala K, Markovic D, Nadel B, Peng K, Do N, Mangul S, Nadkarni VM, Karlsberg A, Deshpande D, Butte MJ, Asaro L, Agus M, Sapru A. PMID: 37693502; PMCID: PMC10491329.
      View in: PubMed   Mentions:
    21. Analytical code sharing practices in biomedical research. bioRxiv. 2023 Aug 07. Sharma NK, Ayyala R, Deshpande D, Patel YM, Munteanu V, Ciorba D, Fiscutean A, Vahed M, Sarkar A, Guo R, Moore A, Darci-Maher N, Nogoy NA, Abedalthagafi MS, Mangul S. PMID: 37609176; PMCID: PMC10441317.
      View in: PubMed   Mentions:
    22. Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing. Brief Bioinform. 2023 07 20; 24(4). 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, Alachkar H, Ribas A, Mangul S. PMID: 37291798; PMCID: PMC10359085.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    23. Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability. Genome Biol. 2023 05 17; 24(1):119. Sonrel A, Luetge A, Soneson C, Mallona I, Germain PL, Knyazev S, Gilis J, Gerber R, Seurinck R, Paul D, Sonder E, Crowell HL, Fanaswala I, Al-Ajami A, Heidari E, Schmeing S, Milosavljevic S, Saeys Y, Mangul S, Robinson MD. PMID: 37198712; PMCID: PMC10189979.
      View in: PubMed   Mentions: 3     Fields:    
    24. RNA-seq data science: From raw data to effective interpretation. Front Genet. 2023; 14:997383. Deshpande D, Chhugani K, Chang Y, Karlsberg A, Loeffler C, Zhang J, Muszynska A, Munteanu V, Yang H, Rotman J, Tao L, Balliu B, Tseng E, Eskin E, Zhao F, Mohammadi P, P Labaj P, Mangul S. PMID: 36999049; PMCID: PMC10043755.
      View in: PubMed   Mentions: 23  
    25. Scientists without borders: lessons from Ukraine. Gigascience. 2022 12 28; 12. Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüs ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Labaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. PMID: 37496156; PMCID: PMC10372202.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    26. TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles. Gigascience. 2022 12 28; 12. Sarwal V, Brito J, Mangul S, Koslicki D. PMID: 36852763; PMCID: PMC9972184.
      View in: PubMed   Mentions: 1     Fields:    
    27. Remote opportunities for scholars in Ukraine. Science. 2022 12 23; 378(6626):1285-1286. Chhugani K, Frolova A, Salyha Y, Fiscutean A, Zlenko O, Reinsone S, Wolfsberger WW, Ivashchenko OV, Maci M, Dziuba D, Parkhomenko A, Bortz E, Kondrashov F, Labaj PP, Romero V, Hlávka J, Oleksyk TK, Mangul S. PMID: 36548425.
      View in: PubMed   Mentions: 1     Fields:    
    28. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet. 2022 11; 18(11):e1010367. Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, Stuckey A, Salas A, Bello X, Pardo-Seco J, Gómez-Carballa A, Rivero-Calle I, Martinón-Torres F, Ganna A, Karczewski KJ, Veerapen K, Bourgey M, Bourque G, Eveleigh RJ, Forgetta V, Morrison D, Langlais D, Lathrop M, Mooser V, Nakanishi T, Frithiof R, Hultström M, Lipcsey M, Marincevic-Zuniga Y, Nordlund J, Schiabor Barrett KM, Lee W, Bolze A, White S, Riffle S, Tanudjaja F, Sandoval E, Neveux I, Dabe S, Casadei N, Motameny S, Alaamery M, Massadeh S, Aljawini N, Almutairi MS, Arabi YM, Alqahtani SA, Al Harthi FS, Almutairi A, Alqubaishi F, Alotaibi S, Binowayn A, Alsolm EA, El Bardisy H, Fawzy M, Cai F, Soranzo N, Butterworth A, COVID-19 Host Genetics Initiative, DeCOI Host Genetics Group, GEN-COVID Multicenter Study (Italy), Mount Sinai Clinical Intelligence Center, GEN-COVID consortium (Spain), GenOMICC Consortium, Japan COVID-19 Task Force, Regeneron Genetics Center, Geschwind DH, Arteaga S, Stephens A, Butte MJ, Boutros PC, Yamaguchi TN, Tao S, Eng S, Sanders T, Tung PJ, Broudy ME, Pan Y, Gonzalez A, Chavan N, Johnson R, Pasaniuc B, Yaspan B, Smieszek S, Rivolta C, Bibert S, Bochud PY, Dabrowski M, Zawadzki P, Sypniewski M, Kaja E, Chariyavilaskul P, Nilaratanakul V, Hirankarn N, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Tokunaga K, Sugiyama M, Kawai Y, Hasegawa T, Naito T, Namkoong H, Edahiro R, Kimura A, Ogawa S, Kanai T, Fukunaga K, Okada Y, Imoto S, Miyano S, Mangul S, Abedalthagafi MS, Zeberg H, Grzymski JJ, Washington NL, Ossowski S, Ludwig KU, Schulte EC, Riess O, Moniuszko M, Kwasniewski M, Mbarek H, Ismail SI, Verma A, Goldstein DB, Kiryluk K, Renieri A, Ferreira MAR, Richards JB. PMID: 36327219; PMCID: PMC9632827.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    29. pyTCR: A comprehensive and scalable solution for TCR-Seq data analysis to facilitate reproducibility and rigor of immunogenomics research. Front Immunol. 2022; 13:954078. Peng K, Moore J, Vahed M, Brito J, Kao G, Burkhardt AM, Alachkar H, Mangul S. PMID: 36451811; PMCID: PMC9704496.
      View in: PubMed   Mentions: 2     Fields:    
    30. The Pioneer Advantage: Filling the blank spots on the map of genome diversity in Europe. Gigascience. 2022 09 09; 11. Oleksyk TK, Wolfsberger WW, Schubelka K, Mangul S, O'Brien SJ. PMID: 36085557; PMCID: PMC9463063.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    31. A comprehensive benchmarking of WGS-based deletion structural variant callers. Brief Bioinform. 2022 07 18; 23(4). Sarwal V, Niehus S, Ayyala R, Kim M, Sarkar A, Chang S, Lu A, Rajkumar N, Darfci-Maher N, Littman R, Chhugani K, Soylev A, Comarova Z, Wesel E, Castellanos J, Chikka R, Distler MG, Eskin E, Flint J, Mangul S. PMID: 35753701; PMCID: PMC9294411.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansAnimals
    32. Critical Assessment of Metagenome Interpretation: the second round of challenges. Nat Methods. 2022 04; 19(4):429-440. 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, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. PMID: 35396482; PMCID: PMC9007738.
      View in: PubMed   Mentions: 115     Fields:    Translation:Cells
    33. Unlocking capacities of genomics for the COVID-19 response and future pandemics. Nat Methods. 2022 04; 19(4):374-380. 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, Sun R, Wu A, Abedalthagafi MS, Pak VM, Nagaraj SH, Smith AL, Skums P, Pasaniuc B, Komissarov A, Mason CE, Bortz E, Lemey P, Kondrashov F, Beerenwinkel N, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. PMID: 35396471; PMCID: PMC9467803.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansCellsPHPublic Health
    34. Correction for Rando et al., "Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure". mSystems. 2022 Feb 22; 7(1):e0144721. Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, D'Agostino McGowan L, Ben Guebila M, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, COVID-19 Review Consortium, Gitter A, Greene CS. PMID: 35076276; PMCID: PMC8788317.
      View in: PubMed   Mentions:    Fields:    
    35. Virtual meetings promise to eliminate geographical and administrative barriers and increase accessibility, diversity and inclusivity. Nat Biotechnol. 2022 01; 40(1):133-137. Wu J, Rajesh A, Huang YN, Chhugani K, Acharya R, Peng K, Johnson RD, Fiscutean A, Robles-Espinoza CD, De La Vega FM, Bao R, Mangul S. PMID: 34966181.
      View in: PubMed   Mentions: 11     Fields:    
    36. Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. Brief Bioinform. 2021 11 05; 22(6). Nadel BB, Oliva M, Shou BL, Mitchell K, Ma F, Montoya DJ, Mouton A, Kim-Hellmuth S, Stranger BE, Pellegrini M, Mangul S. PMID: 34346485; PMCID: PMC8768458.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    37. Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure. mSystems. 2021 10 26; 6(5):e0009521. Rando HM, MacLean AL, Lee AJ, Lordan R, Ray S, Bansal V, Skelly AN, Sell E, Dziak JJ, Shinholster L, D'Agostino McGowan L, Ben Guebila M, Wellhausen N, Knyazev S, Boca SM, Capone S, Qi Y, Park Y, Mai D, Sun Y, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, COVID-19 Review Consortium Vikas Bansal, John P. Barton, Simina M. Boca, Joel D. Boerckel, Chri, Gitter A, Greene CS. PMID: 34698547; PMCID: PMC8547481.
      View in: PubMed   Mentions: 30     Fields:    
    38. Ancestral diversity is limited in published T cell receptor sequencing studies. Immunity. 2021 10 12; 54(10):2177-2179. Huang YN, Peng K, Popejoy AB, Hu J, Nowicki TS, Gold SM, Quintana-Murci L, Fuentes-Guajardo M, Shugay M, Greiff V, Burkhardt AM, Alachkar H, Mangul S. PMID: 34644550.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    39. Accurate assembly of minority viral haplotypes from next-generation sequencing through efficient noise reduction. Nucleic Acids Res. 2021 09 27; 49(17):e102. 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; PMCID: PMC8464054.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansCells
    40. Technology dictates algorithms: recent developments in read alignment. Genome Biol. 2021 08 26; 22(1):249. 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, Mutlu O, Mangul S. PMID: 34446078; PMCID: PMC8390189.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    41. Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19. J Clin Invest. 2021 07 15; 131(14). Povysil G, Butler-Laporte G, Shang N, Wang C, Khan A, Alaamery M, Nakanishi T, Zhou S, Forgetta V, Eveleigh RJ, Bourgey M, Aziz N, Jones SJ, Knoppers B, Scherer SW, Strug LJ, Lepage P, Ragoussis J, Bourque G, Alghamdi J, Aljawini N, Albes N, Al-Afghani HM, Alghamdi B, Almutairi MS, Mahmoud ES, Abu-Safieh L, El Bardisy H, Harthi FSA, 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; PMCID: PMC8279578.
      View in: PubMed   Mentions: 46     Fields:    Translation:HumansCells
    42. Diversity in immunogenomics: the value and the challenge. Nat Methods. 2021 06; 18(6):588-591. 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; PMCID: PMC8842483.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    43. Detection of viral gene expression in risk-stratified biopsies reveals no active HPV in cutaneous squamous cell carcinoma. Exp Dermatol. 2021 11; 30(11):1711-1716. 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; PMCID: PMC9639216.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    44. Unlocking capacities of viral genomics for the COVID-19 pandemic response. ArXiv. 2021 Apr 28. Knyazev S, Chhugani K, Sarwal V, Ayyala R, Singh H, Karthikeyan S, Deshpande D, Comarova Z, Lu A, Porozov Y, Wu A, Abedalthagafi MS, Nagaraj SH, Smith AL, Skums P, Ladner J, Lam TT, Wu NC, Zelikovsky A, Knight R, Crandall KA, Mangul S. PMID: 33948451; PMCID: PMC8095210.
      View in: PubMed   Mentions:
    45. Improving the completeness of public metadata accompanying omics studies. Genome Biol. 2021 04 15; 22(1):106. Rajesh A, Chang Y, Abedalthagafi MS, Wong-Beringer A, Love MI, Mangul S. PMID: 33858487; PMCID: PMC8048353.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    46. The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data. Gigascience. 2021 02 16; 10(2). Nadel BB, Lopez D, Montoya DJ, Ma F, Waddel H, Khan MM, Mangul S, Pellegrini M. PMID: 33590863; PMCID: PMC7931818.
      View in: PubMed   Mentions: 24     Fields:    Translation:Animals
    47. 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, Lordan R, 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, Boerckel JD, Brueffer C, Byrd JB, Kamil JP, Wang J, Velazquez R, Szeto GL, Barton JP, Goel RR, Mangul S, Lubiana T, COVID-19 Review Consortium, Gitter A, Greene CS. PMID: 33594340; PMCID: PMC7885912.
      View in: PubMed   Mentions:
    48. 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; PMCID: PMC7573227.
      View in: PubMed   Mentions: 10  
    49. 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; PMCID: PMC7495904.
      View in: PubMed   Mentions: 2     Fields:    
    50. 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; PMCID: PMC8051643.
      View in: PubMed   Mentions: 160     Fields:    Translation:HumansCells
    51. 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; PMCID: PMC7488264.
      View in: PubMed   Mentions: 26     Fields:    
    52. 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; PMCID: PMC7474053.
      View in: PubMed   Mentions: 1     Fields:    
    53. 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; PMCID: PMC7389812.
      View in: PubMed   Mentions: 1     Fields:    
    54. 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; PMCID: PMC7305308.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    55. 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; PMCID: PMC7321885.
      View in: PubMed   Mentions: 323     Fields:    Translation:HumansCells
    56. 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; PMCID: PMC7263079.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    57. 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; PMCID: PMC7140547.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    58. 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; PMCID: PMC7079412.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    59. 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; PMCID: PMC6977584.
      View in: PubMed   Mentions: 1     Fields:    
    60. 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: 1     Fields:    
    61. 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; PMCID: PMC6746439.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    62. 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; PMCID: PMC6605654.
      View in: PubMed   Mentions: 38     Fields:    Translation:Humans
    63. 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; PMCID: PMC6551237.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    64. 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; PMCID: PMC6437167.
      View in: PubMed   Mentions: 59     Fields:    Translation:Humans
    65. 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: 14     Fields:    Translation:Humans
    66. 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; PMCID: PMC6391762.
      View in: PubMed   Mentions: 32     Fields:    
    67. 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; PMCID: PMC6277220.
      View in: PubMed   Mentions: 9  
    68. 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; PMCID: PMC6693441.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansAnimals
    69. 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; PMCID: PMC5943399.
      View in: PubMed   Mentions: 48     Fields:    Translation:Humans
    70. 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
    71. 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; PMCID: PMC5857127.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    72. 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: 9     Fields:    
    73. 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: 5     Fields:    Translation:Humans
    74. 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; PMCID: PMC5467126.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    75. 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; PMCID: PMC5105841.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    76. CRISPR-Mediated VHL Knockout Generates an Improved Model for Metastatic Renal Cell Carcinoma. Sci Rep. 2016 Jun 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; PMCID: PMC4928183.
      View in: PubMed   Mentions: 35     Fields:    Translation:HumansAnimalsCells
    77. 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; PMCID: PMC4120146.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    78. 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; PMCID: PMC4058922.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    79. 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; PMCID: PMC3194189.
      View in: PubMed   Mentions: 47     Fields:    Translation:HumansCells
    80. 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; PMCID: PMC3107792.
      View in: PubMed   Mentions: 82  
    81. 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: 4     Fields:    Translation:HumansCells
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