Profile

My research group works on a broad range of human genetics projects.  I have worked for over 15 years in the field of mitochondrial genetics, and that continues to be my main focus.  Our current projects are on:

The genetics of cognitive impairment in HIV/AIDS patients

The mitochodnrial genetics of diabetes related phenotypes in HIV/AIDS patients

Genetics of atrial fibrillation

New statistical methods of Phenome Wide Association Studies (PheWAS)

 

Diabetics retinopathy and mitochondrial haplogroups

 

We collaborate actively with wet-lab and clinical researchers world-wide.  Much of our current work is based on the BioVU resource, a de-identified version of the Vanderbilt Electronic Medical Record, combined with DNA samples for ggenotyping.

For up-to-date information, see my website.

Publications

The following timeline graph is generated from all co-authored publications.

Featured publications are shown below:

  1. The Role of Mitochondrial DNA Variation in Age-Related Decline in Gait Speed Among Older Men Living With Human Immunodeficiency Virus. Sun J, Brown TT, Samuels DC, Hulgan T, D'Souza G, Jamieson BD, Erlandson KM, Martinson J, Palella FJ, Margolick JB, Kirk GD, Schrack JA (2018) Clin Infect Dis 67(5): 778-784
    › Primary publication · 29481608 (PubMed) · PMC6093993 (PubMed Central)
  2. Mitochondrial Haplogroups Modify the Effect of Diabetes Duration and HbA1c on Proliferative Diabetic Retinopathy Risk in Patients With Type 2 Diabetes. Mitchell SL, Neininger AC, Bruce CN, Chocron IM, Bregman JA, Estopinal CB, Muhammad A, Umfress AC, Jarrell KL, Warden C, Harlow PA, Wellons M, Samuels DC, Brantley MA (2017) Invest Ophthalmol Vis Sci 58(14): 6481-6488
    › Primary publication · 29288266 (PubMed) · PMC5749245 (PubMed Central)
  3. Current Research on Non-Coding Ribonucleic Acid (RNA). Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y (2017) Genes (Basel) 8(12)
    › Primary publication · 29206165 (PubMed) · PMC5748684 (PubMed Central)
  4. The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data. Guo Y, Zhao S, Sheng Q, Samuels DC, Shyr Y (2017) BMC Genomics 18(Suppl 6): 690
    › Primary publication · 28984205 (PubMed) · PMC5629567 (PubMed Central)
  5. Tri-allelic heteroplasmies, DNA-RNA differences and their polynucleotide tract associations in the mitochondrial genome. Zhao S, Samuels DC, Zhao YY, Guo Y (2017) Genomics
    › Primary publication · 28970049 (PubMed)
  6. Estimating relative mitochondrial DNA copy number using high throughput sequencing data. Zhang P, Lehmann BD, Samuels DC, Zhao S, Zhao YY, Shyr Y, Guo Y (2017) Genomics 109(5-6): 457-462
    › Primary publication · 28734953 (PubMed)
  7. Genome-wide association study of HIV-associated neurocognitive disorder (HAND): A CHARTER group study. Jia P, Zhao Z, Hulgan T, Bush WS, Samuels DC, Bloss CS, Heaton RK, Ellis RJ, Schork N, Marra CM, Collier AC, Clifford DB, Gelman BB, Sacktor N, Morgello S, Simpson DM, McCutchan JA, Barnholtz-Sloan JS, Franklin DR, Rosario D, Letendre SL, Grant I, Kallianpur AR, CHARTER Study Group (2017) Am J Med Genet B Neuropsychiatr Genet 174(4): 413-426
    › Primary publication · 28447399 (PubMed) · PMC5435520 (PubMed Central)
  8. Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults. Patton SM, Wang Q, Hulgan T, Connor JR, Jia P, Zhao Z, Letendre SL, Ellis RJ, Bush WS, Samuels DC, Franklin DR, Kaur H, Iudicello J, Grant I, Kallianpur AR (2017) Fluids Barriers CNS 14(1): 11
    › Primary publication · 28427421 (PubMed) · PMC5399327 (PubMed Central)
  9. StrandScript: evaluation of Illumina genotyping array design and strand correction. Wang J, Samuels DC, Shyr Y, Guo Y (2017) Bioinformatics 33(15): 2399-2401
    › Primary publication · 28402386 (PubMed)
  10. European Mitochondrial DNA Haplogroups are Associated with Cerebrospinal Fluid Biomarkers of Inflammation in HIV Infection. Samuels DC, Kallianpur AR, Ellis RJ, Bush WS, Letendre S, Franklin D, Grant I, Hulgan T (2016) Pathog Immun 1(2): 330-351
    › Primary publication · 28317034 (PubMed) · PMC5351881 (PubMed Central)
  11. Mitochondrial Haplogroups Affect Severity But Not Prevalence of Diabetic Retinopathy. Bregman JA, Herren DJ, Estopinal CB, Chocron IM, Harlow PA, Warden C, Brantley MA, Samuels DC (2017) Invest Ophthalmol Vis Sci 58(2): 1346-1351
    › Primary publication · 28245487 (PubMed) · PMC5341621 (PubMed Central)
  12. OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans. Sierra B, Triska P, Soares P, Garcia G, Perez AB, Aguirre E, Oliveira M, Cavadas B, Regnault B, Alvarez M, Ruiz D, Samuels DC, Sakuntabhai A, Pereira L, Guzman MG (2017) PLoS Pathog 13(2): e1006220
    › Primary publication · 28241052 (PubMed) · PMC5344536 (PubMed Central)
  13. Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis. Guo Y, Dai Y, Yu H, Zhao S, Samuels DC, Shyr Y (2017) Genomics 109(2): 83-90
    › Primary publication · 28131802 (PubMed)
  14. Mitochondrial Haplogroups as a Risk Factor for Herpes Zoster. Levinson RT, Hulgan T, Kalams SA, Fessel JP, Samuels DC (2016) Open Forum Infect Dis 3(4): ofw184
    › Primary publication · 27807590 (PubMed) · PMC5088697 (PubMed Central)
  15. Practicability of mitochondrial heteroplasmy detection through an Illumina genotyping array. Zhang P, Samuels DC, Zhao S, Wang J, Shyr Y, Guo Y (2016) Mitochondrion : 75-78
    › Primary publication · 27628068 (PubMed)
  16. Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk. Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capra JA, Shyr Y, Zheng W, Guo Y (2016) Genetics 204(3): 893-904
    › Primary publication · 27585849 (PubMed) · PMC5105867 (PubMed Central)
  17. Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans. Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR (2016) Cell Metab 24(1): 91-103
    › Primary publication · 27411011 (PubMed) · PMC5287496 (PubMed Central)
  18. Mitochondria single nucleotide variation across six blood cell types. Zhang P, Samuels DC, Wang J, Zhao S, Shyr Y, Guo Y (2016) Mitochondrion : 16-22
    › Primary publication · 26956645 (PubMed) · PMC5755964 (PubMed Central)
  19. Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck. Wilson IJ, Carling PJ, Alston CL, Floros VI, Pyle A, Hudson G, Sallevelt SC, Lamperti C, Carelli V, Bindoff LA, Samuels DC, Wonnapinij P, Zeviani M, Taylor RW, Smeets HJ, Horvath R, Chinnery PF (2016) Hum Mol Genet 25(5): 1031-41
    › Primary publication · 26740552 (PubMed) · PMC4754047 (PubMed Central)
  20. RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library. Guo Y, Zhao S, Sheng Q, Guo M, Lehmann B, Pietenpol J, Samuels DC, Shyr Y (2015) Biomed Res Int : 862130
    › Primary publication · 26543871 (PubMed) · PMC4620295 (PubMed Central)
  21. Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs. Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L (2015) Hum Mutat 36(11): 1100-11
    › Primary publication · 26252938 (PubMed)
  22. Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data. Zhang P, Samuels DC, Lehmann B, Stricker T, Pietenpol J, Shyr Y, Guo Y (2016) Brief Bioinform 17(2): 224-32
    › Primary publication · 26249222 (PubMed) · PMC5974936 (PubMed Central)
  23. Mitochondrial DNA Haplogroups and Neurocognitive Impairment During HIV Infection. Hulgan T, Samuels DC, Bush W, Ellis RJ, Letendre SL, Heaton RK, Franklin DR, Straub P, Murdock DG, Clifford DB, Collier AC, Gelman BB, Marra CM, McArthur JC, McCutchan JA, Morgello S, Simpson DM, Grant I, Kallianpur AR, CHARTER Group (2015) Clin Infect Dis 61(9): 1476-84
    › Primary publication · 26129753 (PubMed) · PMC4599391 (PubMed Central)
  24. Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential. Pereira L, Soares P, Triska P, Rito T, van der Waerden A, Li B, Radivojac P, Samuels DC (2014) Sci Rep : 7155
    › Primary publication · 25412673 (PubMed) · PMC4239565 (PubMed Central)
  25. Illumina human exome genotyping array clustering and quality control. Guo Y, He J, Zhao S, Wu H, Zhong X, Sheng Q, Samuels DC, Shyr Y, Long J (2014) Nat Protoc 9(11): 2643-62
    › Primary publication · 25321409 (PubMed) · PMC4441213 (PubMed Central)
  26. Genome measures used for quality control are dependent on gene function and ancestry. Wang J, Raskin L, Samuels DC, Shyr Y, Guo Y (2015) Bioinformatics 31(3): 318-23
    › Primary publication · 25297068 (PubMed) · PMC4308666 (PubMed Central)
  27. Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy. Kallianpur AR, Jia P, Ellis RJ, Zhao Z, Bloss C, Wen W, Marra CM, Hulgan T, Simpson DM, Morgello S, McArthur JC, Clifford DB, Collier AC, Gelman BB, McCutchan JA, Franklin D, Samuels DC, Rosario D, Holzinger E, Murdock DG, Letendre S, Grant I, CHARTER Study Group (2014) PLoS One 9(8): e103123
    › Primary publication · 25144566 (PubMed) · PMC4140681 (PubMed Central)
  28. Mitochondrial haplogroups are associated with severity of diabetic retinopathy. Estopinal CB, Chocron IM, Parks MB, Wade EA, Roberson RM, Burgess LG, Brantley MA, Samuels DC (2014) Invest Ophthalmol Vis Sci 55(9): 5589-95
    › Primary publication · 25118268 (PubMed) · PMC4160073 (PubMed Central)
  29. High-throughput sequencing in mitochondrial DNA research. Ye F, Samuels DC, Clark T, Guo Y (2014) Mitochondrion : 157-63
    › Primary publication · 24859348 (PubMed) · PMC4149223 (PubMed Central)
  30. Data from artificial models of mitochondrial DNA disorders are not always applicable to humans. Steffann J, Gigarel N, Samuels DC, Monnot S, Borghese R, Hesters L, Frydman N, Burlet P, Frydman R, Benachi A, Rotig A, Munnich A, Bonnefont JP (2014) Cell Rep 7(4): 933-4
    › Primary publication · 24856293 (PubMed)
  31. Epidermal nerve fiber density, oxidative stress, and mitochondrial haplogroups in HIV-infected Thais initiating therapy. Hulgan T, Levinson RT, Gerschenson M, Phanuphak N, Ananworanich J, Teeratakulpisarm N, Jadwattanakul T, LiButti DE, Fink H, McArthur JC, Ebenezer GJ, Hauer P, Murdock D, Shikuma CM, Samuels DC, SEARCH 003 Study Team (2014) AIDS 28(11): 1625-33
    › Primary publication · 24785954 (PubMed) · PMC4427899 (PubMed Central)
  32. Multi-perspective quality control of Illumina exome sequencing data using QC3. Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann B, Pietenpol J, Samuels DC, Shyr Y (2014) Genomics 103(5-6): 323-8
    › Primary publication · 24703969 (PubMed) · PMC5755963 (PubMed Central)
  33. High proportion of heteroresistance in gyrA and gyrB in fluoroquinolone-resistant Mycobacterium tuberculosis clinical isolates. Eilertson B, Maruri F, Blackman A, Herrera M, Samuels DC, Sterling TR (2014) Antimicrob Agents Chemother 58(6): 3270-5
    › Primary publication · 24687490 (PubMed) · PMC4068501 (PubMed Central)
  34. The effect of unhealthy β-cells on insulin secretion in pancreatic islets. Pu Y, Lee S, Samuels DC, Watson LT, Cao Y (2013) BMC Med Genomics : S6
    › Primary publication · 24565418 (PubMed) · PMC3981690 (PubMed Central)
  35. The other genome: a systematic review of studies of mitochondrial DNA haplogroups and outcomes of HIV infection and antiretroviral therapy. Hart AB, Samuels DC, Hulgan T (2013) AIDS Rev 15(4): 213-20
    › Primary publication · 24322381 (PubMed) · PMC4001077 (PubMed Central)
  36. Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control. Guo Y, Sheng Q, Samuels DC, Lehmann B, Bauer JA, Pietenpol J, Shyr Y (2013) Biomed Res Int : 915636
    › Primary publication · 24303503 (PubMed) · PMC3835197 (PubMed Central)
  37. Recurrent tissue-specific mtDNA mutations are common in humans. Samuels DC, Li C, Li B, Song Z, Torstenson E, Boyd Clay H, Rokas A, Thornton-Wells TA, Moore JH, Hughes TM, Hoffman RD, Haines JL, Murdock DG, Mortlock DP, Williams SM (2013) PLoS Genet 9(11): e1003929
    › Primary publication · 24244193 (PubMed) · PMC3820769 (PubMed Central)
  38. Mitochondrial DNA rearrangements in health and disease--a comprehensive study. Damas J, Samuels DC, Carneiro J, Amorim A, Pereira F (2014) Hum Mutat 35(1): 1-14
    › Primary publication · 24115352 (PubMed)
  39. Three-stage quality control strategies for DNA re-sequencing data. Guo Y, Ye F, Sheng Q, Clark T, Samuels DC (2014) Brief Bioinform 15(6): 879-89
    › Primary publication · 24067931 (PubMed) · PMC4492405 (PubMed Central)
  40. Use of a promiscuous, constitutively-active bacterial enhancer-binding protein to define the σ⁵⁴ (RpoN) regulon of Salmonella Typhimurium LT2. Samuels DJ, Frye JG, Porwollik S, McClelland M, Mrázek J, Hoover TR, Karls AC (2013) BMC Genomics : 602
    › Primary publication · 24007446 (PubMed) · PMC3844500 (PubMed Central)
  41. Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y (2013) PLoS One 8(8): e71462
    › Primary publication · 23977046 (PubMed) · PMC3748065 (PubMed Central)
  42. Finding the lost treasures in exome sequencing data. Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y (2013) Trends Genet 29(10): 593-9
    › Primary publication · 23972387 (PubMed) · PMC3926691 (PubMed Central)
  43. Evaluating purifying selection in the mitochondrial DNA of various mammalian species. Soares P, Abrantes D, Rito T, Thomson N, Radivojac P, Li B, Macaulay V, Samuels DC, Pereira L (2013) PLoS One 8(3): e58993
    › Primary publication · 23533597 (PubMed) · PMC3606437 (PubMed Central)
  44. Evaluation of allele frequency estimation using pooled sequencing data simulation. Guo Y, Samuels DC, Li J, Clark T, Li CI, Shyr Y (2013) ScientificWorldJournal : 895496
    › Primary publication · 23476151 (PubMed) · PMC3582166 (PubMed Central)
  45. MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. Guo Y, Li J, Li CI, Shyr Y, Samuels DC (2013) Bioinformatics 29(9): 1210-1
    › Primary publication · 23471301 (PubMed) · PMC4492415 (PubMed Central)
  46. Mitochondrial genomics and antiretroviral therapy-associated metabolic complications in HIV-infected Black South Africans: a pilot study. Sinxadi PZ, Dave JA, Samuels DC, Heckmann JM, Maartens G, Levitt NS, Wester CW, Haas DW, Hulgan T (2013) AIDS Res Hum Retroviruses 29(7): 1031-9
    › Primary publication · 23428049 (PubMed) · PMC3685683 (PubMed Central)
  47. Mutation dependance of the mitochondrial DNA copy number in the first stages of human embryogenesis. Monnot S, Samuels DC, Hesters L, Frydman N, Gigarel N, Burlet P, Kerbrat V, Lamazou F, Frydman R, Benachi A, Feingold J, Rotig A, Munnich A, Bonnefont JP, Steffann J (2013) Hum Mol Genet 22(9): 1867-72
    › Primary publication · 23390135 (PubMed)
  48. Preventing the transmission of pathogenic mitochondrial DNA mutations: Can we achieve long-term benefits from germ-line gene transfer? Samuels DC, Wonnapinij P, Chinnery PF (2013) Hum Reprod 28(3): 554-9
    › Primary publication · 23297368 (PubMed) · PMC3571501 (PubMed Central)
  49. Non-random mtDNA segregation patterns indicate a metastable heteroplasmic segregation unit in m.3243A>G cybrid cells. Raap AK, Jahangir Tafrechi RS, van de Rijke FM, Pyle A, Wählby C, Szuhai K, Ravelli RB, de Coo RF, Rajasimha HK, Nilsson M, Chinnery PF, Samuels DC, Janssen GM (2012) PLoS One 7(12): e52080
    › Primary publication · 23272214 (PubMed) · PMC3525564 (PubMed Central)
  50. What is influencing the phenotype of the common homozygous polymerase-γ mutation p.Ala467Thr? Neeve VC, Samuels DC, Bindoff LA, van den Bosch B, Van Goethem G, Smeets H, Lombès A, Jardel C, Hirano M, Dimauro S, De Vries M, Smeitink J, Smits BW, de Coo IF, Saft C, Klopstock T, Keiling BC, Czermin B, Abicht A, Lochmüller H, Hudson G, Gorman GG, Turnbull DM, Taylor RW, Holinski-Feder E, Chinnery PF, Horvath R (2012) Brain 135(Pt 12): 3614-26
    › Primary publication · 23250882 (PubMed) · PMC3525059 (PubMed Central)
  51. The effect of strand bias in Illumina short-read sequencing data. Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y (2012) BMC Genomics : 666
    › Primary publication · 23176052 (PubMed) · PMC3532123 (PubMed Central)
  52. Universal heteroplasmy of human mitochondrial DNA. Payne BA, Wilson IJ, Yu-Wai-Man P, Coxhead J, Deehan D, Horvath R, Taylor RW, Samuels DC, Santibanez-Koref M, Chinnery PF (2013) Hum Mol Genet 22(2): 384-90
    › Primary publication · 23077218 (PubMed) · PMC3526165 (PubMed Central)
  53. Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER. Holzinger ER, Hulgan T, Ellis RJ, Samuels DC, Ritchie MD, Haas DW, Kallianpur AR, Bloss CS, Clifford DB, Collier AC, Gelman BB, Marra CM, McArthur JC, McCutchan JA, Morgello S, Simpson DM, Franklin DR, Rosario D, Selph D, Letendre S, Grant I, CHARTER Group (2012) J Neurovirol 18(6): 511-20
    › Primary publication · 23073667 (PubMed) · PMC3587171 (PubMed Central)
  54. Variation in germline mtDNA heteroplasmy is determined prenatally but modified during subsequent transmission. Freyer C, Cree LM, Mourier A, Stewart JB, Koolmeister C, Milenkovic D, Wai T, Floros VI, Hagström E, Chatzidaki EE, Wiesner RJ, Samuels DC, Larsson NG, Chinnery PF (2012) Nat Genet 44(11): 1282-5
    › Primary publication · 23042113 (PubMed) · PMC3492742 (PubMed Central)
  55. No evidence of an association between mitochondrial DNA variants and osteoarthritis in 7393 cases and 5122 controls. Hudson G, Panoutsopoulou K, Wilson I, Southam L, Rayner NW, Arden N, Birrell F, Carluke I, Carr A, Chapman K, Deloukas P, Doherty M, McCaskie A, Ollier WE, Ralston SH, Reed MR, Spector TD, Valdes AM, Wallis GA, Wilkinson JM, Zeggini E, Samuels DC, Loughlin J, Chinnery PF, arcOGEN Consortium (2013) Ann Rheum Dis 72(1): 136-9
    › Primary publication · 22984172 (PubMed) · PMC3551219 (PubMed Central)
  56. T cell activation markers and African mitochondrial DNA haplogroups among non-Hispanic black participants in AIDS clinical trials group study 384. Hulgan T, Robbins GK, Kalams SA, Samuels DC, Grady B, Shafer R, Murdock DG, Selph D, Haas DW, Pollard RB, AIDS Clinical Trials Group (2012) PLoS One 7(8): e43803
    › Primary publication · 22970105 (PubMed) · PMC3433792 (PubMed Central)
  57. Mitochondrial DNA deletions are associated with non-B DNA conformations. Damas J, Carneiro J, Gonçalves J, Stewart JB, Samuels DC, Amorim A, Pereira F (2012) Nucleic Acids Res 40(16): 7606-21
    › Primary publication · 22661583 (PubMed) · PMC3439893 (PubMed Central)
  58. Unique mitochondrial DNA in highly inbred feral cattle. Hudson G, Wilson I, Payne BI, Elson J, Samuels DC, Santibanez-Korev M, Hall SJ, Chinnery PF (2012) Mitochondrion 12(4): 438-40
    › Primary publication · 22609322 (PubMed) · PMC3485552 (PubMed Central)
  59. Adult-onset spinocerebellar ataxia syndromes due to MTATP6 mutations. Pfeffer G, Blakely EL, Alston CL, Hassani A, Boggild M, Horvath R, Samuels DC, Taylor RW, Chinnery PF (2012) J Neurol Neurosurg Psychiatry 83(9): 883-6
    › Primary publication · 22577227 (PubMed) · PMC4034166 (PubMed Central)
  60. Risk factors for symptomatic hyperlactatemia and lactic acidosis among combination antiretroviral therapy-treated adults in Botswana: results from a clinical trial. Wester CW, Eden SK, Shepherd BE, Bussmann H, Novitsky V, Samuels DC, Hendrickson SL, Winkler CA, O'Brien SJ, Essex M, D'Aquila RT, DeGruttola V, Marlink RG (2012) AIDS Res Hum Retroviruses 28(8): 759-65
    › Primary publication · 22540188 (PubMed) · PMC3399551 (PubMed Central)
  61. The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation. Guo Y, Cai Q, Samuels DC, Ye F, Long J, Li CI, Winther JF, Tawn EJ, Stovall M, Lähteenmäki P, Malila N, Levy S, Shaffer C, Shyr Y, Shu XO, Boice JD (2012) Mutat Res 744(2): 154-60
    › Primary publication · 22387842 (PubMed) · PMC3354959 (PubMed Central)
  62. Correlated tissue expression of genes of cytoplasmic and mitochondrial nucleotide metabolisms in normal tissues is disrupted in transformed tissues. Gandhi VV, Samuels DC (2012) Nucleosides Nucleotides Nucleic Acids 31(2): 112-29
    › Primary publication · 22303991 (PubMed) · PMC3464496 (PubMed Central)
  63. Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype: pathogenicity analysis of reported somatic mtDNA mutations in tumors. Pereira L, Soares P, Máximo V, Samuels DC (2012) BMC Cancer : 53
    › Primary publication · 22299657 (PubMed) · PMC3342922 (PubMed Central)
  64. Epigenetics, epidemiology and mitochondrial DNA diseases. Chinnery PF, Elliott HR, Hudson G, Samuels DC, Relton CL (2012) Int J Epidemiol 41(1): 177-87
    › Primary publication · 22287136 (PubMed) · PMC3304530 (PubMed Central)
  65. Replication pauses of the wild-type and mutant mitochondrial DNA polymerase gamma: a simulation study. Song Z, Cao Y, Samuels DC (2011) PLoS Comput Biol 7(11): e1002287
    › Primary publication · 22125488 (PubMed) · PMC3219627 (PubMed Central)
  66. Enzyme kinetics of the mitochondrial deoxyribonucleoside salvage pathway are not sufficient to support rapid mtDNA replication. Gandhi VV, Samuels DC (2011) PLoS Comput Biol 7(8): e1002078
    › Primary publication · 21829339 (PubMed) · PMC3150320 (PubMed Central)
  67. Mitochondrial genomics and CD4 T-cell count recovery after antiretroviral therapy initiation in AIDS clinical trials group study 384. Grady BJ, Samuels DC, Robbins GK, Selph D, Canter JA, Pollard RB, Haas DW, Shafer R, Kalams SA, Murdock DG, Ritchie MD, Hulgan T, ACTG 384 and DACS 250 Study Teams (2011) J Acquir Immune Defic Syndr 58(4): 363-70
    › Primary publication · 21792066 (PubMed) · PMC3204178 (PubMed Central)
  68. A review comparing deoxyribonucleoside triphosphate (dNTP) concentrations in the mitochondrial and cytoplasmic compartments of normal and transformed cells. Gandhi VV, Samuels DC (2011) Nucleosides Nucleotides Nucleic Acids 30(5): 317-39
    › Primary publication · 21774628 (PubMed) · PMC3210641 (PubMed Central)
  69. Mitochondrial aging is accelerated by anti-retroviral therapy through the clonal expansion of mtDNA mutations. Payne BA, Wilson IJ, Hateley CA, Horvath R, Santibanez-Koref M, Samuels DC, Price DA, Chinnery PF (2011) Nat Genet 43(8): 806-10
    › Primary publication · 21706004 (PubMed) · PMC3223397 (PubMed Central)
  70. Poor correlations in the levels of pathogenic mitochondrial DNA mutations in polar bodies versus oocytes and blastomeres in humans. Gigarel N, Hesters L, Samuels DC, Monnot S, Burlet P, Kerbrat V, Lamazou F, Benachi A, Frydman R, Feingold J, Rotig A, Munnich A, Bonnefont JP, Frydman N, Steffann J (2011) Am J Hum Genet 88(4): 494-8
    › Primary publication · 21473984 (PubMed) · PMC3071907 (PubMed Central)
  71. Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity. Pereira L, Soares P, Radivojac P, Li B, Samuels DC (2011) Am J Hum Genet 88(4): 433-9
    › Primary publication · 21457906 (PubMed) · PMC3071914 (PubMed Central)
  72. POLG mutations cause decreased mitochondrial DNA repopulation rates following induced depletion in human fibroblasts. Stewart JD, Schoeler S, Sitarz KS, Horvath R, Hallmann K, Pyle A, Yu-Wai-Man P, Taylor RW, Samuels DC, Kunz WS, Chinnery PF (2011) Biochim Biophys Acta 1812(3): 321-5
    › Primary publication · 21138766 (PubMed)
  73. The Bcl-2-associated death promoter (BAD) lowers the threshold at which the Bcl-2-interacting domain death agonist (BID) triggers mitochondria disintegration. Howells CC, Baumann WT, Samuels DC, Finkielstein CV (2011) J Theor Biol 271(1): 114-23
    › Primary publication · 21130780 (PubMed)
  74. Segregation of mtDNA throughout human embryofetal development: m.3243A>G as a model system. Monnot S, Gigarel N, Samuels DC, Burlet P, Hesters L, Frydman N, Frydman R, Kerbrat V, Funalot B, Martinovic J, Benachi A, Feingold J, Munnich A, Bonnefont JP, Steffann J (2011) Hum Mutat 32(1): 116-25
    › Primary publication · 21120938 (PubMed) · PMC3058134 (PubMed Central)
  75. Reassessing evidence for a postnatal mitochondrial genetic bottleneck. Samuels DC, Wonnapinij P, Cree LM, Chinnery PF (2010) Nat Genet 42(6): 471-2; author reply 472-3
    › Primary publication · 20502486 (PubMed)
  76. OPA1 mutations cause cytochrome c oxidase deficiency due to loss of wild-type mtDNA molecules. Yu-Wai-Man P, Sitarz KS, Samuels DC, Griffiths PG, Reeve AK, Bindoff LA, Horvath R, Chinnery PF (2010) Hum Mol Genet 19(15): 3043-52
    › Primary publication · 20484224 (PubMed) · PMC2901142 (PubMed Central)
  77. Previous estimates of mitochondrial DNA mutation level variance did not account for sampling error: comparing the mtDNA genetic bottleneck in mice and humans. Wonnapinij P, Chinnery PF, Samuels DC (2010) Am J Hum Genet 86(4): 540-50
    › Primary publication · 20362273 (PubMed) · PMC2850432 (PubMed Central)
  78. Analysis of enzyme kinetic data for mtDNA replication. Song Z, Samuels DC (2010) Methods 51(4): 385-91
    › Primary publication · 20188839 (PubMed) · PMC2903644 (PubMed Central)
  79. Information for genetic management of mtDNA disease: sampling pathogenic mtDNA mutants in the human germline and in placenta. Marchington D, Malik S, Banerjee A, Turner K, Samuels D, Macaulay V, Oakeshott P, Fratter C, Kennedy S, Poulton J (2010) J Med Genet 47(4): 257-61
    › Primary publication · 19914907 (PubMed)
  80. Detecting new neurodegenerative disease genes: does phenotype accuracy limit the horizon? Samuels DC, Burn DJ, Chinnery PF (2009) Trends Genet 25(11): 486-8
    › Primary publication · 19819581 (PubMed) · PMC2824109 (PubMed Central)
  81. The diversity present in 5140 human mitochondrial genomes. Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, Costa S, Máximo V, Macaulay V, Rocha R, Samuels DC (2009) Am J Hum Genet 84(5): 628-40
    › Primary publication · 19426953 (PubMed) · PMC2681004 (PubMed Central)
  82. The inheritance of pathogenic mitochondrial DNA mutations. Cree LM, Samuels DC, Chinnery PF (2009) Biochim Biophys Acta 1792(12): 1097-102
    › Primary publication · 19303927 (PubMed) · PMC2785871 (PubMed Central)
  83. Discrete stochastic simulation methods for chemically reacting systems. Cao Y, Samuels DC (2009) Methods Enzymol : 115-40
    › Primary publication · 19216925 (PubMed) · PMC3492891 (PubMed Central)
  84. An analysis of enzyme kinetics data for mitochondrial DNA strand termination by nucleoside reverse transcription inhibitors. Wendelsdorf KV, Song Z, Cao Y, Samuels DC (2009) PLoS Comput Biol 5(1): e1000261
    › Primary publication · 19132079 (PubMed) · PMC2603287 (PubMed Central)
  85. The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo. Guan X, Silva P, Gyenai KB, Xu J, Geng T, Tu Z, Samuels DC, Smith EJ (2009) Anim Genet 40(2): 134-41
    › Primary publication · 19067672 (PubMed) · PMC2664387 (PubMed Central)
  86. The distribution of mitochondrial DNA heteroplasmy due to random genetic drift. Wonnapinij P, Chinnery PF, Samuels DC (2008) Am J Hum Genet 83(5): 582-93
    › Primary publication · 18976726 (PubMed) · PMC2668051 (PubMed Central)
  87. Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region. Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, Amorim A (2008) Mol Biol Evol 25(12): 2759-70
    › Primary publication · 18845547 (PubMed)
  88. Pathogenic mitochondrial DNA mutations are common in the general population. Elliott HR, Samuels DC, Eden JA, Relton CL, Chinnery PF (2008) Am J Hum Genet 83(2): 254-60
    › Primary publication · 18674747 (PubMed) · PMC2495064 (PubMed Central)
  89. What causes mitochondrial DNA deletions in human cells? Krishnan KJ, Reeve AK, Samuels DC, Chinnery PF, Blackwood JK, Taylor RW, Wanrooij S, Spelbrink JN, Lightowlers RN, Turnbull DM (2008) Nat Genet 40(3): 275-9
    › Primary publication · 18305478 (PubMed)
  90. The evidence that the DNC (SLC25A19) is not the mitochondrial deoxyribonucleotide carrier. Kang J, Samuels DC (2008) Mitochondrion 8(2): 103-8
    › Primary publication · 18280798 (PubMed)
  91. Selection against pathogenic mtDNA mutations in a stem cell population leads to the loss of the 3243A-->G mutation in blood. Rajasimha HK, Chinnery PF, Samuels DC (2008) Am J Hum Genet 82(2): 333-43
    › Primary publication · 18252214 (PubMed) · PMC2427290 (PubMed Central)
  92. A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes. Cree LM, Samuels DC, de Sousa Lopes SC, Rajasimha HK, Wonnapinij P, Mann JR, Dahl HH, Chinnery PF (2008) Nat Genet 40(2): 249-54
    › Primary publication · 18223651 (PubMed)
  93. Normal levels of wild-type mitochondrial DNA maintain cytochrome c oxidase activity for two pathogenic mitochondrial DNA mutations but not for m.3243A-->G. Durham SE, Samuels DC, Cree LM, Chinnery PF (2007) Am J Hum Genet 81(1): 189-95
    › Primary publication · 17564976 (PubMed) · PMC1950909 (PubMed Central)
  94. Computational models of antiviral toxicity. Samuels DC (2007) Curr Opin Drug Discov Devel 10(1): 43-8
    › Primary publication · 17265740 (PubMed)
  95. Depletion of mitochondrial DNA in leucocytes harbouring the 3243A->G mtDNA mutation. Pyle A, Taylor RW, Durham SE, Deschauer M, Schaefer AM, Samuels DC, Chinnery PF (2007) J Med Genet 44(1): 69-74
    › Primary publication · 16950816 (PubMed) · PMC2597915 (PubMed Central)
  96. Mitochondrial AZT metabolism. Samuels DC (2006) IUBMB Life 58(7): 403-8
    › Primary publication · 16801215 (PubMed)
  97. Is selection required for the accumulation of somatic mitochondrial DNA mutations in post-mitotic cells? Durham SE, Samuels DC, Chinnery PF (2006) Neuromuscul Disord 16(6): 381-6
    › Primary publication · 16684599 (PubMed)
  98. The power to detect disease associations with mitochondrial DNA haplogroups. Samuels DC, Carothers AD, Horton R, Chinnery PF (2006) Am J Hum Genet 78(4): 713-20
    › Primary publication · 16532401 (PubMed) · PMC1424681 (PubMed Central)
  99. Mitochondrial-encoded membrane protein transcripts are pyrimidine-rich while soluble protein transcripts and ribosomal RNA are purine-rich. Bradshaw PC, Rathi A, Samuels DC (2005) BMC Genomics : 136
    › Primary publication · 16185363 (PubMed) · PMC1262711 (PubMed Central)
  100. Mitochondrial DNA copy number threshold in mtDNA depletion myopathy. Durham SE, Bonilla E, Samuels DC, DiMauro S, Chinnery PF (2005) Neurology 65(3): 453-5
    › Primary publication · 16087914 (PubMed)
  101. A computational model of mitochondrial AZT metabolism. Bradshaw PC, Li J, Samuels DC (2005) Biochem J 392(Pt 2): 363-73
    › Primary publication · 16060859 (PubMed) · PMC1316272 (PubMed Central)
  102. Life span is related to the free energy of mitochondrial DNA. Samuels DC (2005) Mech Ageing Dev 126(10): 1123-9
    › Primary publication · 15992863 (PubMed)
  103. A computational model of mitochondrial deoxynucleotide metabolism and DNA replication. Bradshaw PC, Samuels DC (2005) Am J Physiol Cell Physiol 288(5): C989-1002
    › Primary publication · 15634740 (PubMed)
  104. Two direct repeats cause most human mtDNA deletions. Samuels DC, Schon EA, Chinnery PF (2004) Trends Genet 20(9): 393-8
    › Primary publication · 15313545 (PubMed)
  105. Mitochondrial DNA repeats constrain the life span of mammals. Samuels DC (2004) Trends Genet 20(5): 226-9
    › Primary publication · 15109774 (PubMed)
  106. Mitochondrial DNA mutations in human colonic crypt stem cells. Taylor RW, Barron MJ, Borthwick GM, Gospel A, Chinnery PF, Samuels DC, Taylor GA, Plusa SM, Needham SJ, Greaves LC, Kirkwood TB, Turnbull DM (2003) J Clin Invest 112(9): 1351-60
    › Primary publication · 14597761 (PubMed) · PMC228466 (PubMed Central)
  107. A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate. Samuels DC, Boys RJ, Henderson DA, Chinnery PF (2003) Nucleic Acids Res 31(20): 6043-52
    › Primary publication · 14530452 (PubMed) · PMC219467 (PubMed Central)
  108. A model of the nuclear control of mitochondrial DNA replication. Capps GJ, Samuels DC, Chinnery PF (2003) J Theor Biol 221(4): 565-83
    › Primary publication · 12713941 (PubMed)
  109. Polarization of superfluid turbulence. Barenghi CF, Hulton S, Samuels DC (2002) Phys Rev Lett 89(27): 275301
    › Primary publication · 12513214 (PubMed)
  110. Accumulation of mitochondrial DNA mutations in ageing, cancer, and mitochondrial disease: is there a common mechanism? Chinnery PF, Samuels DC, Elson J, Turnbull DM (2002) Lancet 360(9342): 1323-5
    › Primary publication · 12414225 (PubMed)
  111. The length of cytochrome c oxidase-negative segments in muscle fibres in patients with mtDNA myopathy. Elson JL, Samuels DC, Johnson MA, Turnbull DM, Chinnery PF (2002) Neuromuscul Disord 12(9): 858-64
    › Primary publication · 12398838 (PubMed)
  112. Evaporation of a packet of quantized vorticity. Barenghi CF, Samuels DC (2002) Phys Rev Lett 89(15): 155302
    › Primary publication · 12365997 (PubMed)
  113. Quantum signature of superfluid turbulence. Kivotides D, Vassilicos JC, Barenghi CF, Khan MA, Samuels DC (2001) Phys Rev Lett 87(27 Pt 1): 275302
    › Primary publication · 11800889 (PubMed)
  114. Fractal dimension of superfluid turbulence. Kivotides D, Barenghi CF, Samuels DC (2001) Phys Rev Lett 87(15): 155301
    › Primary publication · 11580706 (PubMed)
  115. Sound emission due to superfluid vortex reconnections. Leadbeater M, Winiecki T, Samuels DC, Barenghi CF, Adams CS (2001) Phys Rev Lett 86(8): 1410-3
    › Primary publication · 11290155 (PubMed)
  116. Kelvin waves cascade in superfluid turbulence. Kivotides D, Vassilicos JC, Samuels DC, Barenghi CF (2001) Phys Rev Lett 86(14): 3080-3
    › Primary publication · 11290112 (PubMed)
  117. Random intracellular drift explains the clonal expansion of mitochondrial DNA mutations with age. Elson JL, Samuels DC, Turnbull DM, Chinnery PF (2001) Am J Hum Genet 68(3): 802-6
    › Primary publication · 11179029 (PubMed) · PMC1274494 (PubMed Central)
  118. Random genetic drift determines the level of mutant mtDNA in human primary oocytes. Brown DT, Samuels DC, Michael EM, Turnbull DM, Chinnery PF (2001) Am J Hum Genet 68(2): 533-6
    › Primary publication · 11133360 (PubMed) · PMC1235288 (PubMed Central)
  119. The inheritance of mitochondrial DNA heteroplasmy: random drift, selection or both? Chinnery PF, Thorburn DR, Samuels DC, White SL, Dahl HM, Turnbull DM, Lightowlers RN, Howell N (2000) Trends Genet 16(11): 500-5
    › Primary publication · 11074292 (PubMed)
  120. Triple vortex ring structure in superfluid helium II. Kivotides D, Barenghi CF, Samuels DC (2000) Science 290(5492): 777-9
    › Primary publication · 11052935 (PubMed)
  121. Relaxed replication of mtDNA: A model with implications for the expression of disease. Chinnery PF, Samuels DC (1999) Am J Hum Genet 64(4): 1158-65
    › Primary publication · 10090901 (PubMed) · PMC1377840 (PubMed Central)
  122. Motion of charged vortex rings in helium II. Samuels DC, Donnelly RJ (1991) Phys Rev Lett 67(18): 2505-2508
    › Primary publication · 10044443 (PubMed)
  123. Dynamics of the interactions of rotons with quantized vortices in helium II. Samuels DC, Donnelly RJ (1990) Phys Rev Lett 65(2): 187-190
    › Primary publication · 10042575 (PubMed)
  124. Sideband instability and recurrence of Kelvin waves on vortex cores. Samuels DC, Donnelly RJ (1990) Phys Rev Lett 64(12): 1385-1388
    › Primary publication · 10041382 (PubMed)
  125. Response of superfluid vortex filaments to concentrated normal-fluid vorticity. Samuels DC (1993) Phys Rev B Condens Matter 47(2): 1107-1110
    › Primary publication · 10005596 (PubMed)
  126. Velocity matching and Poiseuille pipe flow of superfluid helium. Samuels DC (1992) Phys Rev B Condens Matter 46(18): 11714-11724
    › Primary publication · 10003062 (PubMed)
  127. The axon as a metabolic compartment: protein degradation, transport, and maximum length of an axon. Miller KE, Samuels DC (1997) J Theor Biol 186(3): 373-9
    › Primary publication · 9219672 (PubMed)
  128. The origin of neuronal polarization: a model of axon formation. Samuels DC, Hentschel HG, Fine A (1996) Philos Trans R Soc Lond B Biol Sci 351(1344): 1147-56
    › Primary publication · 8899865 (PubMed)