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Mark Eppinger

TitleAssistant Professor
InstitutionUniversity of Texas at San Antonio
AddressOnce UTSA Circle
San Antonio TX 78249
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    InstitutionUniversity of Texas at San Antonio
    DepartmentSouth Texas Center for Emerging Infectious Diseases

    Collapse Overview 
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    The focus of Dr. Eppinger’s research is on the application of microbial genomics to address fundamental questions in emerging infectious diseases research. His current interests are directed towards large-scale sequencing and phylogenomic studies investigating major public health threats, such as the causative agents of plague (Yersinia pestis) and cholera (Vibrio cholera) and the dominant cause of food-borne disease in North America, Escherichia coli O157:H7. Experimental approaches include:
    Microbial Genome Sequencing – the gathering of additional sequence data as prerequisite to capture the genome architecture and genomic diversity in environmental or clinical settings
    Phylogenomics – the development of bioinformatics tools to survey the plasticity within pathogen populations and elucidate the ancestry of microbial species
    Microbial Diversity – the discovery of subtle yet important genetic variations in gene content and activity
    Pathogenicity – the study of virulence determinants and dynamic host-pathogen interactions
    Data from this research provides crucial insights into the make-up of bacterial pathogens and how genomic variants relate to differences in evolutionary and ecological niches that underlie human transmissibility, infectivity and disease outcome. Most importantly, this research can help to initiate therapeutic and diagnostic countermeasures in an attempt to decrease human morbidity rates.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    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. Nicholson TL, Waack U, Anderson TK, Bayles DO, Zaia SR, Goertz I, Eppinger M, Hau SJ, Brockmeier SL, Shore SM. Comparative Virulence and Genomic Analysis of Streptococcus suis Isolates. Front Microbiol. 2020; 11:620843. PMID: 33574803.
    2. Petro CD, Duncan JK, Seldina YI, Allué-Guardia A, Eppinger M, Riddle MS, Tribble DR, Johnson RC, Dalgard CL, Sukumar G, Connor P, Boisen N, Melton-Celsa AR. Genetic and Virulence Profiles of Enteroaggregative Escherichia coli (EAEC) Isolated From Deployed Military Personnel (DMP) With Travelers' Diarrhea. Front Cell Infect Microbiol. 2020; 10:200. PMID: 32509590.
      Citations: 2     Fields:    
    3. Nyong EC, Zaia SR, Allué-Guardia A, Rodriguez AL, Irion-Byrd Z, Koenig SSK, Feng P, Bono JL, Eppinger M. Pathogenomes of Atypical Non-shigatoxigenic Escherichia coli NSF/SF O157:H7/NM: Comprehensive Phylogenomic Analysis Using Closed Genomes. Front Microbiol. 2020; 11:619. PMID: 32351476.
    4. Hammad AM, Hoffmann M, Gonzalez-Escalona N, Abbas NH, Yao K, Koenig S, Allué-Guardia A, Eppinger M. Genomic features of colistin resistant Escherichia coli ST69 strain harboring mcr-1 on IncHI2 plasmid from raw milk cheese in Egypt. Infect Genet Evol. 2019 09; 73:126-131. PMID: 31029792.
      Citations: 8     Fields:    Translation:CellsPHPublic Health
    5. Allué-Guardia A, Nyong EC, Koenig SSK, Vargas SM, Bono JL, Eppinger M. Closed Genome Sequence of Escherichia coli K-12 Group Strain C600. Microbiol Resour Announc. 2019 Jan; 8(2). PMID: 30643872.
    6. Hau SJ, Allué-Guardia A, Rusconi B, Haan JS, Davies PR, Frana TS, Eppinger M, Nicholson TL. Single Nucleotide Polymorphism Analysis Indicates Genetic Distinction and Reduced Diversity of Swine-Associated Methicillin Resistant Staphylococcus aureus (MRSA) ST5 Isolates Compared to Clinical MRSA ST5 Isolates. Front Microbiol. 2018; 9:2078. PMID: 30271385.
    7. Allué-Guardia A, Koenig SSK, Quirós P, Muniesa M, Bono JL, Eppinger M. Closed Genome and Comparative Phylogenetic Analysis of the Clinical Multidrug Resistant Shigella sonnei Strain 866. Genome Biol Evol. 2018 09 01; 10(9):2241-2247. PMID: 30060169.
      Citations: 2     Fields:    Translation:HumansCells
    8. Ketter PM, Yu JJ, Guentzel MN, May HC, Gupta R, Eppinger M, Klose KE, Seshu J, Chambers JP, Cap AP, Arulanandam BP. Acinetobacter baumannii Gastrointestinal Colonization Is Facilitated by Secretory IgA Which Is Reductively Dissociated by Bacterial Thioredoxin A. mBio. 2018 07 10; 9(4). PMID: 29991584.
      Citations: 3     Fields:    Translation:AnimalsCells
    9. Allué-Guardia A, Echazarreta M, Koenig SSK, Klose KE, Eppinger M. Closed Genome Sequence of Vibrio cholerae O1 El Tor Inaba Strain A1552. Genome Announc. 2018 Mar 01; 6(9). PMID: 29496831.
    10. DiMarzio M, Rusconi B, Yennawar NH, Eppinger M, Patterson AD, Dudley EG. Identification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-ß-MCA. PLoS One. 2017; 12(9):e0183564. PMID: 28910295.
      Citations: 3     Fields:    Translation:AnimalsCells
    11. Shah MS, Eppinger M, Ahmed S, Shah AA, Hameed A, Hasan F. Flooding adds pathogenic Escherichia coli strains to the water sources in southern Khyber Pakhtunkhwa, Pakistan. Indian J Med Microbiol. 2016 Oct-Dec; 34(4):483-488. PMID: 27934827.
      Citations:    Fields:    Translation:HumansCellsPHPublic Health
    12. Rusconi B, Sanjar F, Koenig SS, Mammel MK, Tarr PI, Eppinger M. Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks. Front Microbiol. 2016; 7:985. PMID: 27446025.
    13. Choi SY, Rashed SM, Hasan NA, Alam M, Islam T, Sadique A, Johura FT, Eppinger M, Ravel J, Huq A, Cravioto A, Colwell RR. Phylogenetic Diversity of Vibrio cholerae Associated with Endemic Cholera in Mexico from 1991 to 2008. mBio. 2016 Mar 15; 7(2):e02160. PMID: 26980836.
      Citations: 7     Fields:    Translation:HumansCellsPHPublic Health
    14. Lopez LL, Rusconi B, Gildersleeve H, Qi C, McLaughlin M, Scheetz MH, Seshu J, Eppinger M. Genome Sequences of Five Clinical Isolates of Klebsiella pneumoniae. Genome Announc. 2016 Mar 10; 4(2). PMID: 26966211.
    15. Yin S, Rusconi B, Sanjar F, Goswami K, Xiaoli L, Eppinger M, Dudley EG. Escherichia coli O157:H7 strains harbor at least three distinct sequence types of Shiga toxin 2a-converting phages. BMC Genomics. 2015 Sep 29; 16:733. PMID: 26416807.
      Citations: 12     Fields:    Translation:HumansCells
    16. Rusconi B, Chen Y, Koenig SS, El-Helow ER, Eppinger M. Genome Sequence of Bacillus thuringiensis Strain Btm27, an Egyptian Isolate Highly Toxic to Cotton Leafworm. Genome Announc. 2015 May 14; 3(3). PMID: 25977430.
    17. Sanjar F, Rusconi B, Hazen TH, Koenig SS, Mammel MK, Feng PC, Rasko DA, Eppinger M. Characterization of the pathogenome and phylogenomic classification of enteropathogenic Escherichia coli of the O157:non-H7 serotypes. Pathog Dis. 2015 Jul; 73(5). PMID: 25962987.
      Citations: 6     Fields:    Translation:HumansCellsPHPublic Health
    18. Jenkins C, Dallman TJ, Launders N, Willis C, Byrne L, Jorgensen F, Eppinger M, Adak GK, Aird H, Elviss N, Grant KA, Morgan D, McLauchlin J. Public Health Investigation of Two Outbreaks of Shiga Toxin-Producing Escherichia coli O157 Associated with Consumption of Watercress. Appl Environ Microbiol. 2015 Jun 15; 81(12):3946-52. PMID: 25841005.
      Citations: 25     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    19. Eppinger M, Pearson T, Koenig SS, Pearson O, Hicks N, Agrawal S, Sanjar F, Galens K, Daugherty S, Crabtree J, Hendriksen RS, Price LB, Upadhyay BP, Shakya G, Fraser CM, Ravel J, Keim PS. Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic. mBio. 2014 Nov 04; 5(6):e01721. PMID: 25370488.
      Citations: 28     Fields:    Translation:CellsPHPublic Health
    20. Eppinger M, Cebula TA. Future perspectives, applications and challenges of genomic epidemiology studies for food-borne pathogens: A case study of Enterohemorrhagic Escherichia coli (EHEC) of the O157:H7 serotype. Gut Microbes. 2015; 6(3):194-201. PMID: 25483335.
      Citations: 9     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    21. Sadiq SM, Hazen TH, Rasko DA, Eppinger M. EHEC Genomics: Past, Present, and Future. Microbiol Spectr. 2014 Aug; 2(4):EHEC-0020-2013. PMID: 26104203.
      Citations: 12     Fields:    Translation:Cells
    22. Khmaladze E, Birdsell DN, Naumann AA, Hochhalter CB, Seymour ML, Nottingham R, Beckstrom-Sternberg SM, Beckstrom-Sternberg J, Nikolich MP, Chanturia G, Zhgenti E, Zakalashvili M, Malania L, Babuadze G, Tsertsvadze N, Abazashvili N, Kekelidze M, Tsanava S, Imnadze P, Ganz HH, Getz WM, Pearson O, Gajer P, Eppinger M, Ravel J, Wagner DM, Okinaka RT, Schupp JM, Keim P, Pearson T. Phylogeography of Bacillus anthracis in the country of Georgia shows evidence of population structuring and is dissimilar to other regional genotypes. PLoS One. 2014; 9(7):e102651. PMID: 25047912.
      Citations: 8     Fields:    Translation:HumansCells
    23. Franz E, Delaquis P, Morabito S, Beutin L, Gobius K, Rasko DA, Bono J, French N, Osek J, Lindstedt BA, Muniesa M, Manning S, LeJeune J, Callaway T, Beatson S, Eppinger M, Dallman T, Forbes KJ, Aarts H, Pearl DL, Gannon VP, Laing CR, Strachan NJ. Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems. Int J Food Microbiol. 2014 Sep 18; 187:57-72. PMID: 25051454.
      Citations: 24     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    24. Dugan VG, Emrich SJ, Giraldo-Calderón GI, Harb OS, Newman RM, Pickett BE, Schriml LM, Stockwell TB, Stoeckert CJ, Sullivan DE, Singh I, Ward DV, Yao A, Zheng J, Barrett T, Birren B, Brinkac L, Bruno VM, Caler E, Chapman S, Collins FH, Cuomo CA, Di Francesco V, Durkin S, Eppinger M, Feldgarden M, Fraser C, Fricke WF, Giovanni M, Henn MR, Hine E, Hotopp JD, Karsch-Mizrachi I, Kissinger JC, Lee EM, Mathur P, Mongodin EF, Murphy CI, Myers G, Neafsey DE, Nelson KE, Nierman WC, Puzak J, Rasko D, Roos DS, Sadzewicz L, Silva JC, Sobral B, Squires RB, Stevens RL, Tallon L, Tettelin H, Wentworth D, White O, Will R, Wortman J, Zhang Y, Scheuermann RH. Standardized metadata for human pathogen/vector genomic sequences. PLoS One. 2014; 9(6):e99979. PMID: 24936976.
      Citations: 17     Fields:    Translation:HumansAnimals
    25. Ketter P, Guentzel MN, Chambers JP, Jorgensen J, Murray CK, Cap AP, Yu JJ, Eppinger M, Arulanandam BP. Genome Sequences of Four Acinetobacter baumannii-A. calcoaceticus Complex Isolates from Combat-Related Infections Sustained in the Middle East. Genome Announc. 2014 Feb 06; 2(1). PMID: 24503987.
    26. Sanjar F, Hazen TH, Shah SM, Koenig SS, Agrawal S, Daugherty S, Sadzewicz L, Tallon LJ, Mammel MK, Feng P, Soderlund R, Tarr PI, Debroy C, Dudley EG, Cebula TA, Ravel J, Fraser CM, Rasko DA, Eppinger M. Genome Sequence of Escherichia coli O157:H7 Strain 2886-75, Associated with the First Reported Case of Human Infection in the United States. Genome Announc. 2014 Jan 09; 2(1). PMID: 24407635.
    27. Eppinger M, McNair K, Zogaj X, Dinsdale EA, Edwards RA, Klose KE. Draft Genome Sequence of the Fish Pathogen Piscirickettsia salmonis. Genome Announc. 2013 Nov 07; 1(6). PMID: 24201203.
    28. Eppinger M, Daugherty S, Agrawal S, Galens K, Sengamalay N, Sadzewicz L, Tallon L, Cebula TA, Mammel MK, Feng P, Soderlund R, Tarr PI, Debroy C, Dudley EG, Fraser CM, Ravel J. Whole-Genome Draft Sequences of 26 Enterohemorrhagic Escherichia coli O157:H7 Strains. Genome Announc. 2013 Feb 28; 1(2):e0013412. PMID: 23516226.
    29. Hasan NA, Choi SY, Eppinger M, Clark PW, Chen A, Alam M, Haley BJ, Taviani E, Hine E, Su Q, Tallon LJ, Prosper JB, Furth K, Hoq MM, Li H, Fraser-Liggett CM, Cravioto A, Huq A, Ravel J, Cebula TA, Colwell RR. Genomic diversity of 2010 Haitian cholera outbreak strains. Proc Natl Acad Sci U S A. 2012 Jul 17; 109(29):E2010-7. PMID: 22711841.
      Citations: 81     Fields:    Translation:HumansCellsPHPublic Health
    30. Earl AM, Eppinger M, Fricke WF, Rosovitz MJ, Rasko DA, Daugherty S, Losick R, Kolter R, Ravel J. Whole-genome sequences of Bacillus subtilis and close relatives. J Bacteriol. 2012 May; 194(9):2378-9. PMID: 22493193.
      Citations: 18     Fields:    Translation:Cells
    31. Eppinger M, Radnedge L, Andersen G, Vietri N, Severson G, Mou S, Ravel J, Worsham PL. Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance. PLoS One. 2012; 7(3):e32911. PMID: 22479347.
      Citations: 4     Fields:    Translation:AnimalsCells
    32. Eppinger M, Mammel MK, Leclerc JE, Ravel J, Cebula TA. Genomic anatomy of Escherichia coli O157:H7 outbreaks. Proc Natl Acad Sci U S A. 2011 Dec 13; 108(50):20142-7. PMID: 22135463.
      Citations: 92     Fields:    Translation:HumansCellsPHPublic Health
    33. Vogler AJ, Chan F, Wagner DM, Roumagnac P, Lee J, Nera R, Eppinger M, Ravel J, Rahalison L, Rasoamanana BW, Beckstrom-Sternberg SM, Achtman M, Chanteau S, Keim P. Phylogeography and molecular epidemiology of Yersinia pestis in Madagascar. PLoS Negl Trop Dis. 2011 Sep; 5(9):e1319. PMID: 21931876.
      Citations: 32     Fields:    Translation:HumansCells
    34. Eppinger M, Bunk B, Johns MA, Edirisinghe JN, Kutumbaka KK, Koenig SS, Creasy HH, Rosovitz MJ, Riley DR, Daugherty S, Martin M, Elbourne LD, Paulsen I, Biedendieck R, Braun C, Grayburn S, Dhingra S, Lukyanchuk V, Ball B, Ul-Qamar R, Seibel J, Bremer E, Jahn D, Ravel J, Vary PS. Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319. J Bacteriol. 2011 Aug; 193(16):4199-213. PMID: 21705586.
      Citations: 48     Fields:    Translation:Cells
    35. Eppinger M, Mammel MK, Leclerc JE, Ravel J, Cebula TA. Genome signatures of Escherichia coli O157:H7 isolates from the bovine host reservoir. Appl Environ Microbiol. 2011 May; 77(9):2916-25. PMID: 21421787.
      Citations: 18     Fields:    Translation:AnimalsCells
    36. Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, Feldkamp M, Kusecek B, Vogler AJ, Li Y, Cui Y, Thomson NR, Jombart T, Leblois R, Lichtner P, Rahalison L, Petersen JM, Balloux F, Keim P, Wirth T, Ravel J, Yang R, Carniel E, Achtman M. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet. 2010 Dec; 42(12):1140-3. PMID: 21037571.
      Citations: 178     Fields:    Translation:Cells
    37. Eppinger M, Worsham PL, Nikolich MP, Riley DR, Sebastian Y, Mou S, Achtman M, Lindler LE, Ravel J. Genome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium. J Bacteriol. 2010 Mar; 192(6):1685-99. PMID: 20061468.
      Citations: 39     Fields:    Translation:AnimalsCells
    38. Eppinger M, Guo Z, Sebastian Y, Song Y, Lindler LE, Yang R, Ravel J. Draft genome sequences of Yersinia pestis isolates from natural foci of endemic plague in China. J Bacteriol. 2009 Dec; 191(24):7628-9. PMID: 19820101.
      Citations: 12     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    39. Myers GS, Mathews SA, Eppinger M, Mitchell C, O'Brien KK, White OR, Benahmed F, Brunham RC, Read TD, Ravel J, Bavoil PM, Timms P. Evidence that human Chlamydia pneumoniae was zoonotically acquired. J Bacteriol. 2009 Dec; 191(23):7225-33. PMID: 19749045.
      Citations: 33     Fields:    Translation:HumansAnimalsCells
    40. Stephens RS, Myers G, Eppinger M, Bavoil PM. Divergence without difference: phylogenetics and taxonomy of Chlamydia resolved. FEMS Immunol Med Microbiol. 2009 Mar; 55(2):115-9. PMID: 19281563.
      Citations: 33     Fields:    Translation:Cells
    41. Auerbach RK, Tuanyok A, Probert WS, Kenefic L, Vogler AJ, Bruce DC, Munk C, Brettin TS, Eppinger M, Ravel J, Wagner DM, Keim P. Yersinia pestis evolution on a small timescale: comparison of whole genome sequences from North America. PLoS One. 2007 Aug 22; 2(8):e770. PMID: 17712418.
      Citations: 18     Fields:    Translation:HumansCells
    42. Eppinger M, Rosovitz MJ, Fricke WF, Rasko DA, Kokorina G, Fayolle C, Lindler LE, Carniel E, Ravel J. The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever. PLoS Genet. 2007 Aug; 3(8):e142. PMID: 17784789.
      Citations: 41     Fields:    Translation:HumansCells
    43. Welch TJ, Fricke WF, McDermott PF, White DG, Rosso ML, Rasko DA, Mammel MK, Eppinger M, Rosovitz MJ, Wagner D, Rahalison L, Leclerc JE, Hinshaw JM, Lindler LE, Cebula TA, Carniel E, Ravel J. Multiple antimicrobial resistance in plague: an emerging public health risk. PLoS One. 2007 Mar 21; 2(3):e309. PMID: 17375195.
      Citations: 157     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    44. Eppinger M, Baar C, Linz B, Raddatz G, Lanz C, Keller H, Morelli G, Gressmann H, Achtman M, Schuster SC. Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet. 2006 Jul; 2(7):e120. PMID: 16789826.
      Citations: 80     Fields:    Translation:HumansAnimalsCells
    45. Eppinger M, Baar C, Raddatz G, Huson DH, Schuster SC. Comparative analysis of four Campylobacterales. Nat Rev Microbiol. 2004 Nov; 2(11):872-85. PMID: 15494744.
      Citations: 46     Fields:    Translation:Cells
    46. Rendulic S, Jagtap P, Rosinus A, Eppinger M, Baar C, Lanz C, Keller H, Lambert C, Evans KJ, Goesmann A, Meyer F, Sockett RE, Schuster SC. A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science. 2004 Jan 30; 303(5658):689-92. PMID: 14752164.
      Citations: 140     Fields:    Translation:Cells
    47. Baar C, Eppinger M, Raddatz G, Simon J, Lanz C, Klimmek O, Nandakumar R, Gross R, Rosinus A, Keller H, Jagtap P, Linke B, Meyer F, Lederer H, Schuster SC. Complete genome sequence and analysis of Wolinella succinogenes. Proc Natl Acad Sci U S A. 2003 Sep 30; 100(20):11690-5. PMID: 14500908.
      Citations: 77     Fields:    Translation:Cells
    48. Deeb GM, Smolens IA, Bolling SF, Eppinger MJ, Pagani FD, Prager RL. Reoperation for Freestyle stentless aortic valves. Semin Thorac Cardiovasc Surg. 2001 Oct; 13(4 Suppl 1):16-23. PMID: 11805944.
      Citations: 3     Fields:    Translation:Humans
    49. Eppinger MJ, Deeb GM, Bolling SF, Ward PA. Mediators of ischemia-reperfusion injury of rat lung. Am J Pathol. 1997 May; 150(5):1773-84. PMID: 9137100.
      Citations: 36     Fields:    Translation:Animals
    50. Eppinger MJ, Ward PA, Bolling SF, Deeb GM. Regulatory effects of interleukin-10 on lung ischemia-reperfusion injury. J Thorac Cardiovasc Surg. 1996 Nov; 112(5):1301-5; discussion 1305-6. PMID: 8911327.
      Citations: 7     Fields:    Translation:AnimalsCells
    51. Eppinger MJ, Ward PA, Jones ML, Bolling SF, Deeb GM. Disparate effects of nitric oxide on lung ischemia-reperfusion injury. Ann Thorac Surg. 1995 Nov; 60(5):1169-75; discussion 1176. PMID: 8526595.
      Citations: 9     Fields:    Translation:AnimalsCells
    52. Eppinger MJ, Jones ML, Deeb GM, Bolling SF, Ward PA. Pattern of injury and the role of neutrophils in reperfusion injury of rat lung. J Surg Res. 1995 Jun; 58(6):713-8. PMID: 7791351.
      Citations: 33     Fields:    Translation:AnimalsCells
    53. Menon AK, Eppinger M, Mayor S, Schwarz RT. Phosphatidylethanolamine is the donor of the terminal phosphoethanolamine group in trypanosome glycosylphosphatidylinositols. EMBO J. 1993 May; 12(5):1907-14. PMID: 8491183.
      Citations: 31     Fields:    Translation:AnimalsCells
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