Faculty Appointments
Associate Professor of Molecular Physiology and Biophysics
Education
Ph.D., Physics, University of Oregon, Eugene, OregonB.A., Physics, Washington University, Saint Louis, Missouri
Office Address
507B Light Hall
2215 Garland Ave.
Nashville, TN 37232
2215 Garland Ave.
Nashville, TN 37232
Research Description
The Samuels group uses computational methods for research on mitochondrial biology and disease. These methods range from biochemical simulations to genetic sequence analysis to clinical data analysis. We collaborate with clinicians and wet-lab biologists.
Our group is applying full-sequence analysis methods to determine the role of mitochondrial DNA variations on various diseases. These include the toxicity of HIV drugs, neurodegenerative diseases, and other phenotypes.
A major current focus is on the genetics of opioid medications, using the Vanderbilt biobank, BioVU.
Our group is applying full-sequence analysis methods to determine the role of mitochondrial DNA variations on various diseases. These include the toxicity of HIV drugs, neurodegenerative diseases, and other phenotypes.
A major current focus is on the genetics of opioid medications, using the Vanderbilt biobank, BioVU.
Research Keywords
Mitochondrial genetics and diseases. Toxicity mechanisms of HIV treatment. Pathogenesis of protein variations. BioVU. Electronic Medical Records. Opioid medications.
Publications
Samuels DC, Hulgan T, Fessel JP, Billings FT, Thompson JL, Chandrasekhar R, Girard TD. Mitochondrial DNA Haplogroups and Delirium During Sepsis. Crit. Care Med. 2019 Aug; 47(8): 1065-71. PMID: 31306254, PII: 00003246-201908000-00008, DOI: 10.1097/CCM.0000000000003810, ISSN: 1530-0293.
Guo M, Yue W, Samuels DC, Yu H, He J, Zhao YY, Guo Y. Quality and concordance of genotyping array data of 12,064 samples from 5840 cancer patients. Genomics [print-electronic]. 2019 Jul; 111(4): 950-7. PMID: 29902512, PMCID: PMC6546549, PII: S0888-7543(18)30201-5, DOI: 10.1016/j.ygeno.2018.06.001, ISSN: 1089-8646.
Kallianpur AR, Gittleman H, Letendre S, Ellis R, Barnholtz-Sloan JS, Bush WS, Heaton R, Samuels DC, Franklin DR, Rosario-Cookson D, Clifford DB, Collier AC, Gelman B, Marra CM, McArthur JC, McCutchan JA, Morgello S, Grant I, Simpson D, Connor JR, Hulgan T, . Cerebrospinal Fluid Ceruloplasmin, Haptoglobin, and Vascular Endothelial Growth Factor Are Associated with Neurocognitive Impairment in Adults with HIV Infection. Mol. Neurobiol [print-electronic]. 2019 May; 56(5): 3808-18. PMID: 30209774, PII: 10.1007/s12035-018-1329-9, DOI: 10.1007/s12035-018-1329-9, ISSN: 1559-1182.
Smieszek S, Jia P, Samuels DC, Zhao Z, Barnholtz-Sloan J, Kaur H, Letendre S, Ellis R, Franklin DR, Hulgan T, Kallianpur A, Bush WS, . Nuclear-Mitochondrial interactions influence susceptibility to HIV-associated neurocognitive impairment. Mitochondrion [print-electronic]. 2019 May; 46: 247-55. PMID: 30026132, PMCID: PMC6336535, PII: S1567-7249(17)30356-2, DOI: 10.1016/j.mito.2018.07.004, ISSN: 1872-8278.
Cavadas B, Pereira JB, Correia M, Fernandes V, Eloy C, Sobrinho-Simões M, Soares P, Samuels DC, Máximo V, Pereira L. Genomic and transcriptomic characterization of the mitochondrial-rich oncocytic phenotype on a thyroid carcinoma background. Mitochondrion [print-electronic]. 2019 May; 46: 123-33. PMID: 29631022, PII: S1567-7249(17)30287-8, DOI: 10.1016/j.mito.2018.04.001, ISSN: 1872-8278.
Chen DQ, Cao G, Chen H, Argyopoulos CP, Yu H, Su W, Chen L, Samuels DC, Zhuang S, Bayliss GP, Zhao S, Yu XY, Vaziri ND, Wang M, Liu D, Mao JR, Ma SX, Zhao J, Zhang Y, Shang YQ, Kang H, Ye F, Cheng XH, Li XR, Zhang L, Meng MX, Guo Y, Zhao YY. Identification of serum metabolites associating with chronic kidney disease progression and anti-fibrotic effect of 5-methoxytryptophan. Nat Commun. 2019 Apr 4/1/2019; 10(1): 1476. PMID: 30931940, PMCID: PMC6443780, PII: 10.1038/s41467-019-09329-0, DOI: 10.1038/s41467-019-09329-0, ISSN: 2041-1723.
Hulgan T, Kallianpur AR, Guo Y, Barnholtz-Sloan JS, Gittleman H, Brown TT, Ellis R, Letendre S, Heaton RK, Samuels DC, . Peripheral Blood Mitochondrial DNA Copy Number Obtained From Genome-Wide Genotype Data Is Associated With Neurocognitive Impairment in Persons With Chronic HIV Infection. J. Acquir. Immune Defic. Syndr. 2019 Apr 4/1/2019; 80(4): e95-e102. PMID: 30531306, PMCID: PMC6391216, DOI: 10.1097/QAI.0000000000001930, ISSN: 1944-7884.
Yu H, Samuels DC, Zhao YY, Guo Y. Architectures and accuracy of artificial neural network for disease classification from omics data. BMC Genomics. 2019 Mar 3/4/2019; 20(1): 167. PMID: 30832569, PMCID: PMC6399893, PII: 10.1186/s12864-019-5546-z, DOI: 10.1186/s12864-019-5546-z, ISSN: 1471-2164.
Hulgan T, Ramsey BS, Koethe JR, Samuels DC, Gerschenson M, Libutti DE, Sax PE, Daar ES, McComsey GA, Brown TT. Relationships Between Adipose Mitochondrial Function, Serum Adiponectin, and Insulin Resistance in Persons With HIV After 96 Weeks of Antiretroviral Therapy. J. Acquir. Immune Defic. Syndr. 2019 Mar 3/1/2019; 80(3): 358-66. PMID: 30531304, PMCID: PMC6375746, DOI: 10.1097/QAI.0000000000001926, ISSN: 1944-7884.
Guo Y, Yu H, Samuels DC, Yue W, Ness S, Zhao YY. Single-nucleotide variants in human RNA: RNA editing and beyond. Brief Funct Genomics. 2019 Feb 2/14/2019; 18(1): 30-9. PMID: 30312373, PII: 5128362, DOI: 10.1093/bfgp/ely032, ISSN: 2041-2657.
Chigaev M, Yu H, Samuels DC, Sheng Q, Oyebamiji O, Ness S, Yue W, Zhao YY, Guo Y. Genomic Positional Dissection of RNA Editomes in Tumor and Normal Samples. Front Genet. 2019; 10: 211. PMID: 30949194, PMCID: PMC6435843, DOI: 10.3389/fgene.2019.00211, ISSN: 1664-8021.
Li CI, Samuels DC, Zhao YY, Shyr Y, Guo Y. Power and sample size calculations for high-throughput sequencing-based experiments. Brief. Bioinformatics. 2018 Nov 11/27/2018; 19(6): 1247-55. PMID: 28605403, PMCID: PMC6291796, PII: 3865509, DOI: 10.1093/bib/bbx061, ISSN: 1477-4054.
Sheng Q, Samuels DC, Yu H, Ness S, Zhao YY, Guo Y. Cancer-specific expression quantitative loci are affected by expression dysregulation. Brief. Bioinformatics [print-electronic]. 2018 Nov 11/23/2018; PMID: 30475999, PII: 5194058, DOI: 10.1093/bib/bby108, ISSN: 1477-4054.
Feng B, Hoskins W, Zhang Y, Meng Z, Samuels DC, Wang J, Xia R, Liu C, Tang J, Guo Y. Bi-stream CNN Down Syndrome screening model based on genotyping array. BMC Med Genomics. 2018 Nov 11/20/2018; 11(Suppl 5): 105. PMID: 30453947, PMCID: PMC6245487, PII: 10.1186/s12920-018-0416-0, DOI: 10.1186/s12920-018-0416-0, ISSN: 1755-8794.
Kallianpur AR, Gerschenson M, Hulgan T, Kaur H, Clifford DB, Haas DW, Murdock DG, McArthur JC, Samuels DC, Simpson DM. Hemochromatosis (HFE) Gene Variants Are Associated with Increased Mitochondrial DNA Levels During HIV-1 Infection and Antiretroviral Therapy. AIDS Res. Hum. Retroviruses [print-electronic]. 2018 Nov; 34(11): 942-9. PMID: 29968489, PMCID: PMC6421985, DOI: 10.1089/AID.2018.0025, ISSN: 1931-8405.
Zhao S, Jing W, Samuels DC, Sheng Q, Shyr Y, Guo Y. Strategies for processing and quality control of Illumina genotyping arrays. Brief. Bioinformatics. 2018 Sep 9/28/2018; 19(5): 765-75. PMID: 28334151, PMCID: PMC6171493, PII: 3038466, DOI: 10.1093/bib/bbx012, ISSN: 1477-4054.
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. The Role of Mitochondrial DNA Variation in Age-Related Decline in Gait Speed Among Older Men Living With Human Immunodeficiency Virus. Clin. Infect. Dis. 2018 Aug 8/16/2018; 67(5): 778-84. PMID: 29481608, PMCID: PMC6093993, PII: 4898130, DOI: 10.1093/cid/ciy151, ISSN: 1537-6591.
Chalazan B, Dickerman D, Sridhar A, Farrell M, Gayle K, Samuels DC, Shoemaker B, Darbar D. Relation of Body Mass Index to Symptom Burden in Patients withAtrial Fibrillation. Am. J. Cardiol [print-electronic]. 2018 Jul 7/15/2018; 122(2): 235-41. PMID: 29914646, PMCID: PMC6028292, PII: S0002-9149(18)30862-2, DOI: 10.1016/j.amjcard.2018.04.011, ISSN: 1879-1913.
Otten ABC, Sallevelt SCEH, Carling PJ, Dreesen JCFM, Drüsedau M, Spierts S, Paulussen ADC, de Die-Smulders CEM, Herbert M, Chinnery PF, Samuels DC, Lindsey P, Smeets HJM. Mutation-specific effects in germline transmission of pathogenic mtDNA variants. Hum. Reprod. 2018 Jul 7/1/2018; 33(7): 1331-41. PMID: 29850888, PMCID: PMC6551225, PII: 5025586, DOI: 10.1093/humrep/dey114, ISSN: 1460-2350.
Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y. Current Research on Non-Coding Ribonucleic Acid (RNA). Genes (Basel). 2017 Dec 12/5/2017; 8(12): PMID: 29206165, PMCID: PMC5748684, PII: genes8120366, DOI: 10.3390/genes8120366, ISSN: 2073-4425.
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. Mitochondrial Haplogroups Modify the Effect of Diabetes Duration and HbA1c on Proliferative Diabetic Retinopathy Risk in Patients With Type 2 Diabetes. Invest. Ophthalmol. Vis. Sci. 2017 Dec 12/1/2017; 58(14): 6481-8. PMID: 29288266, PMCID: PMC5749245, PII: 2668092, DOI: 10.1167/iovs.17-22804, ISSN: 1552-5783.
Guo Y, Zhao S, Sheng Q, Samuels DC, Shyr Y. The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data. BMC Genomics. 2017 Oct 10/3/2017; 18(Suppl 6): 690. PMID: 28984205, PMCID: PMC5629567, PII: 10.1186/s12864-017-4022-x, DOI: 10.1186/s12864-017-4022-x, ISSN: 1471-2164.
Zhao S, Samuels DC, Zhao YY, Guo Y. Tri-allelic heteroplasmies, DNA-RNA differences and their polynucleotide tract associations in the mitochondrial genome. Genomics [print-electronic]. 2017 Sep 9/29/2017; PMID: 28970049, PII: S0888-7543(17)30093-9, DOI: 10.1016/j.ygeno.2017.09.013, ISSN: 1089-8646.
Wang J, Samuels DC, Shyr Y, Guo Y. StrandScript: evaluation of Illumina genotyping array design and strand correction. Bioinformatics. 2017 Aug 8/1/2017; 33(15): 2399-401. PMID: 28402386, PII: 3204987, DOI: 10.1093/bioinformatics/btx186, ISSN: 1367-4811.
Zhang P, Lehmann BD, Samuels DC, Zhao S, Zhao YY, Shyr Y, Guo Y. Estimating relative mitochondrial DNA copy number using high throughput sequencing data. Genomics [print-electronic]. 2017 Jul 7/19/2017; PMID: 28734953, PII: S0888-7543(17)30060-5, DOI: 10.1016/j.ygeno.2017.07.002, ISSN: 1089-8646.
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, . Genome-wide association study of HIV-associated neurocognitive disorder (HAND): A CHARTER group study. Am. J. Med. Genet. B Neuropsychiatr. Genet [print-electronic]. 2017 Jun; 174(4): 413-26. PMID: 28447399, PMCID: PMC5435520, DOI: 10.1002/ajmg.b.32530, ISSN: 1552-485X.
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. Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults. Fluids Barriers CNS. 2017 Apr 4/21/2017; 14(1): 11. PMID: 28427421, PMCID: PMC5399327, PII: 10.1186/s12987-017-0058-1, DOI: 10.1186/s12987-017-0058-1, ISSN: 2045-8118.
Guo Y, Dai Y, Yu H, Zhao S, Samuels DC, Shyr Y. Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis. Genomics [print-electronic]. 2017 Mar; 109(2): 83-90. PMID: 28131802, PII: S0888-7543(17)30005-8, DOI: 10.1016/j.ygeno.2017.01.005, ISSN: 1089-8646.
Bregman JA, Herren DJ, Estopinal CB, Chocron IM, Harlow PA, Warden C, Brantley MA, Samuels DC. Mitochondrial Haplogroups Affect Severity But Not Prevalence of Diabetic Retinopathy. Invest. Ophthalmol. Vis. Sci. 2017 Feb 2/1/2017; 58(2): 1346-51. PMID: 28245487, PMCID: PMC5341621, PII: 2607959, DOI: 10.1167/iovs.16-20616, ISSN: 1552-5783.
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. OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans. PLoS Pathog. 2017 Feb; 13(2): e1006220. PMID: 28241052, PMCID: PMC5344536, PII: PPATHOGENS-D-16-02742, DOI: 10.1371/journal.ppat.1006220, ISSN: 1553-7374.
Zhang P, Samuels DC, Zhao S, Wang J, Shyr Y, Guo Y. Practicability of mitochondrial heteroplasmy detection through an Illumina genotyping array. Mitochondrion [print-electronic]. 2016 Nov; 31: 75-8. PMID: 27628068, PII: S1567-7249(16)30061-7, DOI: 10.1016/j.mito.2016.08.018, ISSN: 1872-8278.
Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capra JA, Shyr Y, Zheng W, Guo Y. Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk. Genetics [print-electronic]. 2016 Nov; 204(3): 893-904. PMID: 27585849, PMCID: PMC5105867, PII: genetics.116.189936, DOI: 10.1534/genetics.116.189936, ISSN: 1943-2631.
Levinson RT, Hulgan T, Kalams SA, Fessel JP, Samuels DC. Mitochondrial Haplogroups as a Risk Factor for Herpes Zoster. Open Forum Infect Dis. 2016 Oct; 3(4): ofw184. PMID: 27807590, PMCID: PMC5088697, PII: ofw184, DOI: 10.1093/ofid/ofw184, ISSN: 2328-8957.
Samuels DC, Kallianpur AR, Ellis RJ, Bush WS, Letendre S, Franklin D, Grant I, Hulgan T. European Mitochondrial DNA Haplogroups are Associated with Cerebrospinal Fluid Biomarkers of Inflammation in HIV Infection. Pathog Immun. 2016 Sep; 1(2): 330-51. PMID: 28317034, PMCID: PMC5351881, DOI: 10.20411/pai.v1i2.156, ISSN: 2469-2964.
Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR. Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans. Cell Metab. 2016 Jul 7/12/2016; 24(1): 91-103. PMID: 27411011, PMCID: PMC5287496, PII: S1550-4131(16)30294-7, DOI: 10.1016/j.cmet.2016.06.008, ISSN: 1932-7420.
Zhang P, Samuels DC, Wang J, Zhao S, Shyr Y, Guo Y. Mitochondria single nucleotide variation across six blood cell types. Mitochondrion [print-electronic]. 2016 May; 28: 16-22. PMID: 26956645, PII: S1567-7249(16)30011-3, DOI: 10.1016/j.mito.2016.03.001, ISSN: 1872-8278.
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. Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck. Hum. Mol. Genet [print-electronic]. 2016 Mar 3/1/2016; 25(5): 1031-41. PMID: 26740552, PMCID: PMC4754047, PII: ddv626, DOI: 10.1093/hmg/ddv626, ISSN: 1460-2083.
Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L. Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs. Hum. Mutat [print-electronic]. 2015 Nov; 36(11): 1100-11. PMID: 26252938, DOI: 10.1002/humu.22849, ISSN: 1098-1004.
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, . Mitochondrial DNA Haplogroups and Neurocognitive Impairment During HIV Infection. Clin. Infect. Dis [print-electronic]. 2015 Nov 11/1/2015; 61(9): 1476-84. PMID: 26129753, PMCID: PMC4599391, PII: civ527, DOI: 10.1093/cid/civ527, ISSN: 1537-6591.
Wang J, Raskin L, Samuels DC, Shyr Y, Guo Y. Genome measures used for quality control are dependent on gene function and ancestry. Bioinformatics [print-electronic]. 2015 Feb 2/1/2015; 31(3): 318-23. PMID: 25297068, PMCID: PMC4308666, PII: btu668, DOI: 10.1093/bioinformatics/btu668, ISSN: 1367-4811.
Guo Y, Zhao S, Sheng Q, Guo M, Lehmann B, Pietenpol J, Samuels DC, Shyr Y. RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library. Biomed Res Int [print-electronic]. 2015; 2015: 862130. PMID: 26543871, PMCID: PMC4620295, DOI: 10.1155/2015/862130, ISSN: 2314-6141.
Guo Y, He J, Zhao S, Wu H, Zhong X, Sheng Q, Samuels DC, Shyr Y, Long J. Illumina human exome genotyping array clustering and quality control. Nat Protoc [print-electronic]. 2014 Nov; 9(11): 2643-62. PMID: 25321409, PMCID: PMC4441213, PII: nprot.2014.174, DOI: 10.1038/nprot.2014.174, ISSN: 1750-2799.
Estopinal CB, Chocron IM, Parks MB, Wade EA, Roberson RM, Burgess LG, Brantley MA, Samuels DC. Mitochondrial haplogroups are associated with severity of diabetic retinopathy. Invest. Ophthalmol. Vis. Sci. 2014 Sep; 55(9): 5589-95. PMID: 25118268, PMCID: PMC4160073, PII: iovs.14-15149, DOI: 10.1167/iovs.14-15149, ISSN: 1552-5783.
Ye F, Samuels DC, Clark T, Guo Y. High-throughput sequencing in mitochondrial DNA research. Mitochondrion [print-electronic]. 2014 Jul; 17: 157-63. PMID: 24859348, PMCID: PMC4149223, PII: S1567-7249(14)00078-6, DOI: 10.1016/j.mito.2014.05.004, ISSN: 1872-8278.
Eilertson B, Maruri F, Blackman A, Herrera M, Samuels DC, Sterling TR. High proportion of heteroresistance in gyrA and gyrB in fluoroquinolone-resistant Mycobacterium tuberculosis clinical isolates. Antimicrob. Agents Chemother [print-electronic]. 2014 Jun; 58(6): 3270-5. PMID: 24687490, PMCID: PMC4068501, PII: AAC.02066-13, DOI: 10.1128/AAC.02066-13, ISSN: 1098-6596.
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. Data from artificial models of mitochondrial DNA disorders are not always applicable to humans [letter]. Cell Rep. 2014 May 5/22/2014; 7(4): 933-4. PMID: 24856293, PII: S2211-1247(14)00380-5, DOI: 10.1016/j.celrep.2014.05.005, ISSN: 2211-1247.
Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann B, Pietenpol J, Samuels DC, Shyr Y. Multi-perspective quality control of Illumina exome sequencing data using QC3. Genomics [print-electronic]. 2014 May; 103(5-6): 323-8. PMID: 24703969, PII: S0888-7543(14)00035-4, DOI: 10.1016/j.ygeno.2014.03.006, ISSN: 1089-8646.
Pereira L, Soares P, Triska P, Rito T, van der Waerden A, Li B, Radivojac P, Samuels DC. Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential. Sci Rep. 2014; 4: 7155. PMID: 25412673, PMCID: PMC4239565, PII: srep07155, DOI: 10.1038/srep07155, ISSN: 2045-2322.
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, . Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy. PLoS ONE. 2014; 9(8): e103123. PMID: 25144566, PMCID: PMC4140681, PII: PONE-D-14-09650, DOI: 10.1371/journal.pone.0103123, ISSN: 1932-6203.
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. Recurrent tissue-specific mtDNA mutations are common in humans. PLoS Genet [print-electronic]. 2013 Nov; 9(11): e1003929. PMID: 24244193, PMCID: PMC3820769, PII: PGENETICS-D-13-01891, DOI: 10.1371/journal.pgen.1003929, ISSN: 1553-7404.
Hart AB, Samuels DC, Hulgan T. The other genome: a systematic review of studies of mitochondrial DNA haplogroups and outcomes of HIV infection and antiretroviral therapy. AIDS Rev. 2013 Oct; 15(4): 213-20. PMID: 24322381, PMCID: PMC4001077, ISSN: 1698-6997.
Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y. Finding the lost treasures in exome sequencing data. Trends Genet [print-electronic]. 2013 Oct; 29(10): 593-9. PMID: 23972387, PMCID: PMC3926691, PII: S0168-9525(13)00127-3, DOI: 10.1016/j.tig.2013.07.006, ISSN: 0168-9525.
Guo Y, Li J, Li CI, Shyr Y, Samuels DC. MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. Bioinformatics [print-electronic]. 2013 May 5/1/2013; 29(9): 1210-1. PMID: 23471301, PMCID: PMC4492415, PII: btt118, DOI: 10.1093/bioinformatics/btt118, ISSN: 1367-4811.
Samuels DC, Wonnapinij P, Chinnery PF. Preventing the transmission of pathogenic mitochondrial DNA mutations: Can we achieve long-term benefits from germ-line gene transfer?. Hum. Reprod [print-electronic]. 2013 Mar; 28(3): 554-9. PMID: 23297368, PMCID: PMC3571501, PII: des439, DOI: 10.1093/humrep/des439, ISSN: 1460-2350.
Guo Y, Sheng Q, Samuels DC, Lehmann B, Bauer JA, Pietenpol J, Shyr Y. Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control. Biomed Res Int [print-electronic]. 2013; 2013: 915636. PMID: 24303503, PMCID: PMC3835197, DOI: 10.1155/2013/915636, ISSN: 2314-6141.
Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y. Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS ONE. 2013; 8(8): e71462. PMID: 23977046, PMCID: PMC3748065, PII: PONE-D-13-05180, DOI: 10.1371/journal.pone.0071462, ISSN: 1932-6203.
Guo Y, Samuels DC, Li J, Clark T, Li CI, Shyr Y. Evaluation of allele frequency estimation using pooled sequencing data simulation. ScientificWorldJournal [print-electronic]. 2013; 2013: 895496. PMID: 23476151, PMCID: PMC3582166, DOI: 10.1155/2013/895496, ISSN: 1537-744X.
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, . Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER. J. Neurovirol [print-electronic]. 2012 Dec; 18(6): 511-20. PMID: 23073667, PMCID: PMC3587171, DOI: 10.1007/s13365-012-0133-y, ISSN: 1538-2443.
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. Risk factors for symptomatic hyperlactatemia and lactic acidosis among combination antiretroviral therapy-treated adults in Botswana: results from a clinical trial. AIDS Res. Hum. Retroviruses [print-electronic]. 2012 Aug; 28(8): 759-65. PMID: 22540188, PMCID: PMC3399551, DOI: 10.1089/AID.2011.0303, ISSN: 1931-8405.
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. The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation. Mutat. Res [print-electronic]. 2012 May 5/15/2012; 744(2): 154-60. PMID: 22387842, PMCID: PMC3354959, PII: S1383-5718(12)00060-5, DOI: 10.1016/j.mrgentox.2012.02.006, ISSN: 0027-5107.
Pereira L, Soares P, Máximo V, Samuels DC. 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. BMC Cancer. 2012 Feb 2/2/2012; 12: 53. PMID: 22299657, PMCID: PMC3342922, PII: 1471-2407-12-53, DOI: 10.1186/1471-2407-12-53, ISSN: 1471-2407.
Chinnery PF, Elliott HR, Hudson G, Samuels DC, Relton CL. Epigenetics, epidemiology and mitochondrial DNA diseases. Int J Epidemiol [print-electronic]. 2012 Feb; 41(1): 177-87. PMID: 22287136, PMCID: PMC3304530, PII: dyr232, DOI: 10.1093/ije/dyr232, ISSN: 1464-3685.
Gandhi VV, Samuels DC. Correlated tissue expression of genes of cytoplasmic and mitochondrial nucleotide metabolisms in normal tissues is disrupted in transformed tissues. Nucleosides Nucleotides Nucleic Acids. 2012; 31(2): 112-29. PMID: 22303991, PMCID: PMC3464496, DOI: 10.1080/15257770.2011.644101, ISSN: 1532-2335.
Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y. The effect of strand bias in Illumina short-read sequencing data. BMC Genomics. 2012; 13: 666. PMID: 23176052, PMCID: PMC3532123, PII: 1471-2164-13-666, DOI: 10.1186/1471-2164-13-666, ISSN: 1471-2164.
Hulgan T, Robbins GK, Kalams SA, Samuels DC, Grady B, Shafer R, Murdock DG, Selph D, Haas DW, Pollard RB, . T cell activation markers and African mitochondrial DNA haplogroups among non-Hispanic black participants in AIDS clinical trials group study 384. PLoS ONE [print-electronic]. 2012; 7(8): e43803. PMID: 22970105, PMCID: PMC3433792, PII: PONE-D-12-11386, DOI: 10.1371/journal.pone.0043803, ISSN: 1932-6203.
Grady BJ, Samuels DC, Robbins GK, Selph D, Canter JA, Pollard RB, Haas DW, Shafer R, Kalams SA, Murdock DG, Ritchie MD, Hulgan T, . Mitochondrial genomics and CD4 T-cell count recovery after antiretroviral therapy initiation in AIDS clinical trials group study 384. J. Acquir. Immune Defic. Syndr. 2011 Dec 12/1/2011; 58(4): 363-70. PMID: 21792066, PMCID: PMC3204178, DOI: 10.1097/QAI.0b013e31822c688b, ISSN: 1944-7884.
Song Z, Cao Y, Samuels DC. Replication pauses of the wild-type and mutant mitochondrial DNA polymerase gamma: a simulation study. PLoS Comput. Biol [print-electronic]. 2011 Nov; 7(11): e1002287. PMID: 22125488, PMCID: PMC3219627, PII: PCOMPBIOL-D-11-00627, DOI: 10.1371/journal.pcbi.1002287, ISSN: 1553-7358.
Gandhi VV, Samuels DC. Enzyme kinetics of the mitochondrial deoxyribonucleoside salvage pathway are not sufficient to support rapid mtDNA replication. PLoS Comput. Biol [print-electronic]. 2011 Aug; 7(8): e1002078. PMID: 21829339, PMCID: PMC3150320, PII: PCOMPBIOL-D-11-00157, DOI: 10.1371/journal.pcbi.1002078, ISSN: 1553-7358.
Gandhi VV, Samuels DC. A review comparing deoxyribonucleoside triphosphate (dNTP) concentrations in the mitochondrial and cytoplasmic compartments of normal and transformed cells. Nucleosides Nucleotides Nucleic Acids. 2011 May; 30(5): 317-39. PMID: 21774628, PMCID: PMC3210641, DOI: 10.1080/15257770.2011.586955, ISSN: 1532-2335.
Howells CC, Baumann WT, Samuels DC, Finkielstein CV. The Bcl-2-associated death promoter (BAD) lowers the threshold at which the Bcl-2-interacting domain death agonist (BID) triggers mitochondria disintegration. J. Theor. Biol [print-electronic]. 2011 Feb 2/21/2011; 271(1): 114-23. PMID: 21130780, PII: S0022-5193(10)00635-1, DOI: 10.1016/j.jtbi.2010.11.040, ISSN: 1095-8541.
Yu-Wai-Man P, Sitarz KS, Samuels DC, Griffiths PG, Reeve AK, Bindoff LA, Horvath R, Chinnery PF. OPA1 mutations cause cytochrome c oxidase deficiency due to loss of wild-type mtDNA molecules. Hum. Mol. Genet [print-electronic]. 2010 Aug 8/1/2010; 19(15): 3043-52. PMID: 20484224, PMCID: PMC2901142, PII: ddq209, DOI: 10.1093/hmg/ddq209, ISSN: 1460-2083.
Song Z, Samuels DC. Analysis of enzyme kinetic data for mtDNA replication. Methods [print-electronic]. 2010 Aug; 51(4): 385-91. PMID: 20188839, PMCID: PMC2903644, PII: S1046-2023(10)00095-2, DOI: 10.1016/j.ymeth.2010.02.019, ISSN: 1095-9130.
Samuels DC, Wonnapinij P, Cree LM, Chinnery PF. Reassessing evidence for a postnatal mitochondrial genetic bottleneck [letter]. Nat. Genet. 2010 Jun; 42(6): 471-2; author reply 472. PMID: 20502486, PII: ng0610-471, DOI: 10.1038/ng0610-471, ISSN: 1546-1718.
Wonnapinij P, Chinnery PF, Samuels DC. Previous estimates of mitochondrial DNA mutation level variance did not account for sampling error: comparing the mtDNA genetic bottleneck in mice and humans. Am. J. Hum. Genet [print-electronic]. 2010 Apr 4/9/2010; 86(4): 540-50. PMID: 20362273, PMCID: PMC2850432, PII: S0002-9297(10)00139-4, DOI: 10.1016/j.ajhg.2010.02.023, ISSN: 1537-6605.
Marchington D, Malik S, Banerjee A, Turner K, Samuels D, Macaulay V, Oakeshott P, Fratter C, Kennedy S, Poulton J. Information for genetic management of mtDNA disease: sampling pathogenic mtDNA mutants in the human germline and in placenta. J. Med. Genet [print-electronic]. 2010 Apr; 47(4): 257-61. PMID: 19914907, PII: jmg.2009.072900, DOI: 10.1136/jmg.2009.072900, ISSN: 1468-6244.
Cree LM, Samuels DC, Chinnery PF. The inheritance of pathogenic mitochondrial DNA mutations. Biochim. Biophys. Acta [print-electronic]. 2009 Dec; 1792(12): 1097-102. PMID: 19303927, PMCID: PMC2785871, PII: S0925-4439(09)00062-3, DOI: 10.1016/j.bbadis.2009.03.002, ISSN: 0006-3002.
Samuels DC, Burn DJ, Chinnery PF. Detecting new neurodegenerative disease genes: does phenotype accuracy limit the horizon? [letter]. Trends Genet [print-electronic]. 2009 Nov; 25(11): 486-8. PMID: 19819581, PMCID: PMC2824109, PII: S0168-9525(09)00181-4, DOI: 10.1016/j.tig.2009.09.008, ISSN: 0168-9525.
Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, Costa S, Máximo V, Macaulay V, Rocha R, Samuels DC. The diversity present in 5140 human mitochondrial genomes. Am. J. Hum. Genet [print-electronic]. 2009 May; 84(5): 628-40. PMID: 19426953, PMCID: PMC2681004, PII: S0002-9297(09)00155-4, DOI: 10.1016/j.ajhg.2009.04.013, ISSN: 1537-6605.
Guan X, Silva P, Gyenai KB, Xu J, Geng T, Tu Z, Samuels DC, Smith EJ. The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo. Anim. Genet [print-electronic]. 2009 Apr; 40(2): 134-41. PMID: 19067672, PMCID: PMC2664387, PII: AGE1810, DOI: 10.1111/j.1365-2052.2008.01810.x, ISSN: 1365-2052.
Cao Y, Samuels DC. Discrete stochastic simulation methods for chemically reacting systems. Meth. Enzymol. 2009; 454: 115-40. PMID: 19216925, PMCID: PMC3492891, PII: S0076-6879(08)03805-6, DOI: 10.1016/S0076-6879(08)03805-6, ISSN: 1557-7988.
Wendelsdorf KV, Song Z, Cao Y, Samuels DC. An analysis of enzyme kinetics data for mitochondrial DNA strand termination by nucleoside reverse transcription inhibitors. PLoS Comput. Biol [print-electronic]. 2009 Jan; 5(1): e1000261. PMID: 19132079, PMCID: PMC2603287, DOI: 10.1371/journal.pcbi.1000261, ISSN: 1553-7358.
Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, Amorim A. Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region. Mol. Biol. Evol [print-electronic]. 2008 Dec; 25(12): 2759-70. PMID: 18845547, PII: msn225, DOI: 10.1093/molbev/msn225, ISSN: 1537-1719.
Wonnapinij P, Chinnery PF, Samuels DC. The distribution of mitochondrial DNA heteroplasmy due to random genetic drift. Am. J. Hum. Genet [print-electronic]. 2008 Nov; 83(5): 582-93. PMID: 18976726, PMCID: PMC2668051, PII: S0002-9297(08)00542-9, DOI: 10.1016/j.ajhg.2008.10.007, ISSN: 1537-6605.
Elliott HR, Samuels DC, Eden JA, Relton CL, Chinnery PF. Pathogenic mitochondrial DNA mutations are common in the general population. Am. J. Hum. Genet. 2008 Aug; 83(2): 254-60. PMID: 18674747, PMCID: PMC2495064, PII: S0002-9297(08)00402-3, DOI: 10.1016/j.ajhg.2008.07.004, ISSN: 1537-6605.
Krishnan KJ, Reeve AK, Samuels DC, Chinnery PF, Blackwood JK, Taylor RW, Wanrooij S, Spelbrink JN, Lightowlers RN, Turnbull DM. What causes mitochondrial DNA deletions in human cells?. Nat. Genet. 2008 Mar; 40(3): 275-9. PMID: 18305478, PII: ng.f.94, DOI: 10.1038/ng.f.94, ISSN: 1546-1718.
Kang J, Samuels DC. The evidence that the DNC (SLC25A19) is not the mitochondrial deoxyribonucleotide carrier. Mitochondrion [print-electronic]. 2008 Mar; 8(2): 103-8. PMID: 18280798, PII: S1567-7249(08)00002-0, DOI: 10.1016/j.mito.2008.01.001, ISSN: 1567-7249.
Rajasimha HK, Chinnery PF, Samuels DC. Selection against pathogenic mtDNA mutations in a stem cell population leads to the loss of the 3243A-->G mutation in blood. Am. J. Hum. Genet. 2008 Feb; 82(2): 333-43. PMID: 18252214, PMCID: PMC2427290, PII: S0002-9297(08)00085-2, DOI: 10.1016/j.ajhg.2007.10.007, ISSN: 1537-6605.
Cree LM, Samuels DC, de Sousa Lopes SC, Rajasimha HK, Wonnapinij P, Mann JR, Dahl HH, Chinnery PF. A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes. Nat. Genet [print-electronic]. 2008 Feb; 40(2): 249-54. PMID: 18223651, PII: ng.2007.63, DOI: 10.1038/ng.2007.63, ISSN: 1546-1718.
Durham SE, Samuels DC, Cree LM, Chinnery PF. Normal levels of wild-type mitochondrial DNA maintain cytochrome c oxidase activity for two pathogenic mitochondrial DNA mutations but not for m.3243A-->G. Am. J. Hum. Genet [print-electronic]. 2007 Jul; 81(1): 189-95. PMID: 17564976, PMCID: PMC1950909, PII: S0002-9297(07)62829-8, DOI: 10.1086/518901, ISSN: 0002-9297.
Samuels DC. Computational models of antiviral toxicity. Curr Opin Drug Discov Devel. 2007 Jan; 10(1): 43-8. PMID: 17265740, ISSN: 1367-6733.
Pyle A, Taylor RW, Durham SE, Deschauer M, Schaefer AM, Samuels DC, Chinnery PF. Depletion of mitochondrial DNA in leucocytes harbouring the 3243A->G mtDNA mutation [letter]. J. Med. Genet [print-electronic]. 2007 Jan; 44(1): 69-74. PMID: 16950816, PMCID: PMC2597915, PII: jmg.2006.043109, DOI: 10.1136/jmg.2006.043109, ISSN: 1468-6244.
Samuels DC. Mitochondrial AZT metabolism. IUBMB Life. 2006 Jul; 58(7): 403-8. PMID: 16801215, PII: K032UV7JUK7V3618, DOI: 10.1080/15216540600791571, ISSN: 1521-6543.
Durham SE, Samuels DC, Chinnery PF. Is selection required for the accumulation of somatic mitochondrial DNA mutations in post-mitotic cells?. Neuromuscul. Disord [print-electronic]. 2006 Jun; 16(6): 381-6. PMID: 16684599, PII: S0960-8966(06)00093-9, DOI: 10.1016/j.nmd.2006.03.012, ISSN: 0960-8966.
Samuels DC, Carothers AD, Horton R, Chinnery PF. The power to detect disease associations with mitochondrial DNA haplogroups. Am. J. Hum. Genet [print-electronic]. 2006 Apr; 78(4): 713-20. PMID: 16532401, PMCID: PMC1424681, PII: S0002-9297(07)63709-4, DOI: 10.1086/502682, ISSN: 0002-9297.
Bradshaw PC, Li J, Samuels DC. A computational model of mitochondrial AZT metabolism. Biochem. J. 2005 Dec 12/1/2005; 392(Pt 2): 363-73. PMID: 16060859, PMCID: PMC1316272, PII: BJ20050749, DOI: 10.1042/BJ20050749, ISSN: 1470-8728.
Samuels DC. Life span is related to the free energy of mitochondrial DNA. Mech. Ageing Dev. 2005 Oct; 126(10): 1123-9. PMID: 15992863, PII: S0047-6374(05)00120-X, DOI: 10.1016/j.mad.2005.05.003, ISSN: 0047-6374.
Durham SE, Bonilla E, Samuels DC, DiMauro S, Chinnery PF. Mitochondrial DNA copy number threshold in mtDNA depletion myopathy. Neurology. 2005 Aug 8/9/2005; 65(3): 453-5. PMID: 16087914, PII: 65/3/453, DOI: 10.1212/01.wnl.0000171861.30277.88, ISSN: 1526-632X.
Bradshaw PC, Samuels DC. A computational model of mitochondrial deoxynucleotide metabolism and DNA replication. Am. J. Physiol., Cell Physiol [print-electronic]. 2005 May; 288(5): C989-1002. PMID: 15634740, PII: 00530.2004, DOI: 10.1152/ajpcell.00530.2004, ISSN: 0363-6143.
Bradshaw PC, Rathi A, Samuels DC. Mitochondrial-encoded membrane protein transcripts are pyrimidine-rich while soluble protein transcripts and ribosomal RNA are purine-rich. BMC Genomics. 2005; 6: 136. PMID: 16185363, PMCID: PMC1262711, PII: 1471-2164-6-136, DOI: 10.1186/1471-2164-6-136, ISSN: 1471-2164.
Samuels DC, Schon EA, Chinnery PF. Two direct repeats cause most human mtDNA deletions. Trends Genet. 2004 Sep; 20(9): 393-8. PMID: 15313545, PII: S0168-9525(04)00183-0, DOI: 10.1016/j.tig.2004.07.003, ISSN: 0168-9525.
Samuels DC. Mitochondrial DNA repeats constrain the life span of mammals. Trends Genet. 2004 May; 20(5): 226-9. PMID: 15109774, PII: S0168-9525(04)00071-X, DOI: 10.1016/j.tig.2004.03.003, ISSN: 0168-9525.
Taylor RW, Barron MJ, Borthwick GM, Gospel A, Chinnery PF, Samuels DC, Taylor GA, Plusa SM, Needham SJ, Greaves LC, Kirkwood TB, Turnbull DM. Mitochondrial DNA mutations in human colonic crypt stem cells. J. Clin. Invest. 2003 Nov; 112(9): 1351-60. PMID: 14597761, PMCID: PMC228466, PII: 112/9/1351, DOI: 10.1172/JCI19435, ISSN: 0021-9738.
Samuels DC, Boys RJ, Henderson DA, Chinnery PF. A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate. Nucleic Acids Res. 2003 Oct 10/15/2003; 31(20): 6043-52. PMID: 14530452, PMCID: PMC219467, ISSN: 1362-4962.
Capps GJ, Samuels DC, Chinnery PF. A model of the nuclear control of mitochondrial DNA replication. J. Theor. Biol. 2003 Apr 4/21/2003; 221(4): 565-83. PMID: 12713941, PII: S0022519303932073, ISSN: 0022-5193.
Barenghi CF, Hulton S, Samuels DC. Polarization of superfluid turbulence. Phys. Rev. Lett [print-electronic]. 2002 Dec 12/30/2002; 89(27): 275301. PMID: 12513214, DOI: 10.1103/PhysRevLett.89.275301, ISSN: 0031-9007.
Elson JL, Samuels DC, Johnson MA, Turnbull DM, Chinnery PF. The length of cytochrome c oxidase-negative segments in muscle fibres in patients with mtDNA myopathy. Neuromuscul. Disord. 2002 Nov; 12(9): 858-64. PMID: 12398838, PII: S0960896602000470, ISSN: 0960-8966.
Chinnery PF, Samuels DC, Elson J, Turnbull DM. Accumulation of mitochondrial DNA mutations in ageing, cancer, and mitochondrial disease: is there a common mechanism?. Lancet. 2002 Oct 10/26/2002; 360(9342): 1323-5. PMID: 12414225, PII: S0140-6736(02)11310-9, DOI: 10.1016/S0140-6736(02)11310-9, ISSN: 0140-6736.
Barenghi CF, Samuels DC. Evaporation of a packet of quantized vorticity. Phys. Rev. Lett [print-electronic]. 2002 Oct 10/7/2002; 89(15): 155302. PMID: 12365997, DOI: 10.1103/PhysRevLett.89.155302, ISSN: 0031-9007.
Kivotides D, Vassilicos JC, Barenghi CF, Khan MA, Samuels DC. Quantum signature of superfluid turbulence. Phys. Rev. Lett [print-electronic]. 2001 Dec 12/31/2001; 87(27 Pt 1): 275302. PMID: 11800889, DOI: 10.1103/PhysRevLett.87.275302, ISSN: 0031-9007.
Kivotides D, Barenghi CF, Samuels DC. Fractal dimension of superfluid turbulence. Phys. Rev. Lett [print-electronic]. 2001 Oct 10/8/2001; 87(15): 155301. PMID: 11580706, DOI: 10.1103/PhysRevLett.87.155301, ISSN: 0031-9007.
Kivotides D, Vassilicos JC, Samuels DC, Barenghi CF. Kelvin waves cascade in superfluid turbulence. Phys. Rev. Lett. 2001 Apr 4/2/2001; 86(14): 3080-3. PMID: 11290112, DOI: 10.1103/PhysRevLett.86.3080, ISSN: 0031-9007.
Elson JL, Samuels DC, Turnbull DM, Chinnery PF. Random intracellular drift explains the clonal expansion of mitochondrial DNA mutations with age. Am. J. Hum. Genet [print-electronic]. 2001 Mar; 68(3): 802-6. PMID: 11179029, PMCID: PMC1274494, PII: S0002-9297(07)63121-8, DOI: 10.1086/318801, ISSN: 0002-9297.
Leadbeater M, Winiecki T, Samuels DC, Barenghi CF, Adams CS. Sound emission due to superfluid vortex reconnections. Phys. Rev. Lett. 2001 Feb 2/19/2001; 86(8): 1410-3. PMID: 11290155, DOI: 10.1103/PhysRevLett.86.1410, ISSN: 0031-9007.
Brown DT, Samuels DC, Michael EM, Turnbull DM, Chinnery PF. Random genetic drift determines the level of mutant mtDNA in human primary oocytes. Am. J. Hum. Genet [print-electronic]. 2001 Feb; 68(2): 533-6. PMID: 11133360, PMCID: PMC1235288, PII: S0002-9297(07)64107-X, DOI: 10.1086/318190, ISSN: 0002-9297.
Chinnery PF, Thorburn DR, Samuels DC, White SL, Dahl HM, Turnbull DM, Lightowlers RN, Howell N. The inheritance of mitochondrial DNA heteroplasmy: random drift, selection or both?. Trends Genet. 2000 Nov; 16(11): 500-5. PMID: 11074292, PII: S016895250002120X, ISSN: 0168-9525.
Kivotides D, Barenghi CF, Samuels DC. Triple vortex ring structure in superfluid helium II. Science. 2000 Oct 10/27/2000; 290(5492): 777-9. PMID: 11052935, PII: 8937, ISSN: 0036-8075.
Chinnery PF, Samuels DC. Relaxed replication of mtDNA: A model with implications for the expression of disease. Am. J. Hum. Genet. 1999 Apr; 64(4): 1158-65. PMID: 10090901, PMCID: PMC1377840, PII: AJHG980454, ISSN: 0002-9297.
Miller KE, Samuels DC. The axon as a metabolic compartment: protein degradation, transport, and maximum length of an axon. J. Theor. Biol. 1997 Jun 6/7/1997; 186(3): 373-9. PMID: 9219672, PII: S0022-5193(96)90355-0, DOI: 10.1006/jtbi.1996.0355, ISSN: 0022-5193.
Samuels DC, Hentschel HG, Fine A. The origin of neuronal polarization: a model of axon formation. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 1996 Sep 9/30/1996; 351(1344): 1147-56. PMID: 8899865, DOI: 10.1098/rstb.1996.0099, ISSN: 0962-8436.
Samuels DC. Response of superfluid vortex filaments to concentrated normal-fluid vorticity. Phys. Rev., B Condens. Matter. 1993 Jan 1/1/1993; 47(2): 1107-10. PMID: 10005596, ISSN: 0163-1829.
Samuels DC. Velocity matching and Poiseuille pipe flow of superfluid helium. Phys. Rev., B Condens. Matter. 1992 Nov 11/1/1992; 46(18): 11714-24. PMID: 10003062, ISSN: 0163-1829.
Samuels DC, Donnelly RJ. Motion of charged vortex rings in helium II. Phys. Rev. Lett. 1991 Oct 10/28/1991; 67(18): 2505-8. PMID: 10044443, DOI: 10.1103/PhysRevLett.67.2505, ISSN: 1079-7114.
Samuels DC, Donnelly RJ. Dynamics of the interactions of rotons with quantized vortices in helium II. Phys. Rev. Lett. 1990 Jul 7/9/1990; 65(2): 187-90. PMID: 10042575, DOI: 10.1103/PhysRevLett.65.187, ISSN: 1079-7114.
Samuels DC, Donnelly RJ. Sideband instability and recurrence of Kelvin waves on vortex cores. Phys. Rev. Lett. 1990 Mar 3/19/1990; 64(12): 1385-8. PMID: 10041382, DOI: 10.1103/PhysRevLett.64.1385, ISSN: 1079-7114.
Guo M, Yue W, Samuels DC, Yu H, He J, Zhao YY, Guo Y. Quality and concordance of genotyping array data of 12,064 samples from 5840 cancer patients. Genomics [print-electronic]. 2019 Jul; 111(4): 950-7. PMID: 29902512, PMCID: PMC6546549, PII: S0888-7543(18)30201-5, DOI: 10.1016/j.ygeno.2018.06.001, ISSN: 1089-8646.
Kallianpur AR, Gittleman H, Letendre S, Ellis R, Barnholtz-Sloan JS, Bush WS, Heaton R, Samuels DC, Franklin DR, Rosario-Cookson D, Clifford DB, Collier AC, Gelman B, Marra CM, McArthur JC, McCutchan JA, Morgello S, Grant I, Simpson D, Connor JR, Hulgan T, . Cerebrospinal Fluid Ceruloplasmin, Haptoglobin, and Vascular Endothelial Growth Factor Are Associated with Neurocognitive Impairment in Adults with HIV Infection. Mol. Neurobiol [print-electronic]. 2019 May; 56(5): 3808-18. PMID: 30209774, PII: 10.1007/s12035-018-1329-9, DOI: 10.1007/s12035-018-1329-9, ISSN: 1559-1182.
Smieszek S, Jia P, Samuels DC, Zhao Z, Barnholtz-Sloan J, Kaur H, Letendre S, Ellis R, Franklin DR, Hulgan T, Kallianpur A, Bush WS, . Nuclear-Mitochondrial interactions influence susceptibility to HIV-associated neurocognitive impairment. Mitochondrion [print-electronic]. 2019 May; 46: 247-55. PMID: 30026132, PMCID: PMC6336535, PII: S1567-7249(17)30356-2, DOI: 10.1016/j.mito.2018.07.004, ISSN: 1872-8278.
Cavadas B, Pereira JB, Correia M, Fernandes V, Eloy C, Sobrinho-Simões M, Soares P, Samuels DC, Máximo V, Pereira L. Genomic and transcriptomic characterization of the mitochondrial-rich oncocytic phenotype on a thyroid carcinoma background. Mitochondrion [print-electronic]. 2019 May; 46: 123-33. PMID: 29631022, PII: S1567-7249(17)30287-8, DOI: 10.1016/j.mito.2018.04.001, ISSN: 1872-8278.
Chen DQ, Cao G, Chen H, Argyopoulos CP, Yu H, Su W, Chen L, Samuels DC, Zhuang S, Bayliss GP, Zhao S, Yu XY, Vaziri ND, Wang M, Liu D, Mao JR, Ma SX, Zhao J, Zhang Y, Shang YQ, Kang H, Ye F, Cheng XH, Li XR, Zhang L, Meng MX, Guo Y, Zhao YY. Identification of serum metabolites associating with chronic kidney disease progression and anti-fibrotic effect of 5-methoxytryptophan. Nat Commun. 2019 Apr 4/1/2019; 10(1): 1476. PMID: 30931940, PMCID: PMC6443780, PII: 10.1038/s41467-019-09329-0, DOI: 10.1038/s41467-019-09329-0, ISSN: 2041-1723.
Hulgan T, Kallianpur AR, Guo Y, Barnholtz-Sloan JS, Gittleman H, Brown TT, Ellis R, Letendre S, Heaton RK, Samuels DC, . Peripheral Blood Mitochondrial DNA Copy Number Obtained From Genome-Wide Genotype Data Is Associated With Neurocognitive Impairment in Persons With Chronic HIV Infection. J. Acquir. Immune Defic. Syndr. 2019 Apr 4/1/2019; 80(4): e95-e102. PMID: 30531306, PMCID: PMC6391216, DOI: 10.1097/QAI.0000000000001930, ISSN: 1944-7884.
Yu H, Samuels DC, Zhao YY, Guo Y. Architectures and accuracy of artificial neural network for disease classification from omics data. BMC Genomics. 2019 Mar 3/4/2019; 20(1): 167. PMID: 30832569, PMCID: PMC6399893, PII: 10.1186/s12864-019-5546-z, DOI: 10.1186/s12864-019-5546-z, ISSN: 1471-2164.
Hulgan T, Ramsey BS, Koethe JR, Samuels DC, Gerschenson M, Libutti DE, Sax PE, Daar ES, McComsey GA, Brown TT. Relationships Between Adipose Mitochondrial Function, Serum Adiponectin, and Insulin Resistance in Persons With HIV After 96 Weeks of Antiretroviral Therapy. J. Acquir. Immune Defic. Syndr. 2019 Mar 3/1/2019; 80(3): 358-66. PMID: 30531304, PMCID: PMC6375746, DOI: 10.1097/QAI.0000000000001926, ISSN: 1944-7884.
Guo Y, Yu H, Samuels DC, Yue W, Ness S, Zhao YY. Single-nucleotide variants in human RNA: RNA editing and beyond. Brief Funct Genomics. 2019 Feb 2/14/2019; 18(1): 30-9. PMID: 30312373, PII: 5128362, DOI: 10.1093/bfgp/ely032, ISSN: 2041-2657.
Chigaev M, Yu H, Samuels DC, Sheng Q, Oyebamiji O, Ness S, Yue W, Zhao YY, Guo Y. Genomic Positional Dissection of RNA Editomes in Tumor and Normal Samples. Front Genet. 2019; 10: 211. PMID: 30949194, PMCID: PMC6435843, DOI: 10.3389/fgene.2019.00211, ISSN: 1664-8021.
Li CI, Samuels DC, Zhao YY, Shyr Y, Guo Y. Power and sample size calculations for high-throughput sequencing-based experiments. Brief. Bioinformatics. 2018 Nov 11/27/2018; 19(6): 1247-55. PMID: 28605403, PMCID: PMC6291796, PII: 3865509, DOI: 10.1093/bib/bbx061, ISSN: 1477-4054.
Sheng Q, Samuels DC, Yu H, Ness S, Zhao YY, Guo Y. Cancer-specific expression quantitative loci are affected by expression dysregulation. Brief. Bioinformatics [print-electronic]. 2018 Nov 11/23/2018; PMID: 30475999, PII: 5194058, DOI: 10.1093/bib/bby108, ISSN: 1477-4054.
Feng B, Hoskins W, Zhang Y, Meng Z, Samuels DC, Wang J, Xia R, Liu C, Tang J, Guo Y. Bi-stream CNN Down Syndrome screening model based on genotyping array. BMC Med Genomics. 2018 Nov 11/20/2018; 11(Suppl 5): 105. PMID: 30453947, PMCID: PMC6245487, PII: 10.1186/s12920-018-0416-0, DOI: 10.1186/s12920-018-0416-0, ISSN: 1755-8794.
Kallianpur AR, Gerschenson M, Hulgan T, Kaur H, Clifford DB, Haas DW, Murdock DG, McArthur JC, Samuels DC, Simpson DM. Hemochromatosis (HFE) Gene Variants Are Associated with Increased Mitochondrial DNA Levels During HIV-1 Infection and Antiretroviral Therapy. AIDS Res. Hum. Retroviruses [print-electronic]. 2018 Nov; 34(11): 942-9. PMID: 29968489, PMCID: PMC6421985, DOI: 10.1089/AID.2018.0025, ISSN: 1931-8405.
Zhao S, Jing W, Samuels DC, Sheng Q, Shyr Y, Guo Y. Strategies for processing and quality control of Illumina genotyping arrays. Brief. Bioinformatics. 2018 Sep 9/28/2018; 19(5): 765-75. PMID: 28334151, PMCID: PMC6171493, PII: 3038466, DOI: 10.1093/bib/bbx012, ISSN: 1477-4054.
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. The Role of Mitochondrial DNA Variation in Age-Related Decline in Gait Speed Among Older Men Living With Human Immunodeficiency Virus. Clin. Infect. Dis. 2018 Aug 8/16/2018; 67(5): 778-84. PMID: 29481608, PMCID: PMC6093993, PII: 4898130, DOI: 10.1093/cid/ciy151, ISSN: 1537-6591.
Chalazan B, Dickerman D, Sridhar A, Farrell M, Gayle K, Samuels DC, Shoemaker B, Darbar D. Relation of Body Mass Index to Symptom Burden in Patients withAtrial Fibrillation. Am. J. Cardiol [print-electronic]. 2018 Jul 7/15/2018; 122(2): 235-41. PMID: 29914646, PMCID: PMC6028292, PII: S0002-9149(18)30862-2, DOI: 10.1016/j.amjcard.2018.04.011, ISSN: 1879-1913.
Otten ABC, Sallevelt SCEH, Carling PJ, Dreesen JCFM, Drüsedau M, Spierts S, Paulussen ADC, de Die-Smulders CEM, Herbert M, Chinnery PF, Samuels DC, Lindsey P, Smeets HJM. Mutation-specific effects in germline transmission of pathogenic mtDNA variants. Hum. Reprod. 2018 Jul 7/1/2018; 33(7): 1331-41. PMID: 29850888, PMCID: PMC6551225, PII: 5025586, DOI: 10.1093/humrep/dey114, ISSN: 1460-2350.
Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y. Current Research on Non-Coding Ribonucleic Acid (RNA). Genes (Basel). 2017 Dec 12/5/2017; 8(12): PMID: 29206165, PMCID: PMC5748684, PII: genes8120366, DOI: 10.3390/genes8120366, ISSN: 2073-4425.
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. Mitochondrial Haplogroups Modify the Effect of Diabetes Duration and HbA1c on Proliferative Diabetic Retinopathy Risk in Patients With Type 2 Diabetes. Invest. Ophthalmol. Vis. Sci. 2017 Dec 12/1/2017; 58(14): 6481-8. PMID: 29288266, PMCID: PMC5749245, PII: 2668092, DOI: 10.1167/iovs.17-22804, ISSN: 1552-5783.
Guo Y, Zhao S, Sheng Q, Samuels DC, Shyr Y. The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data. BMC Genomics. 2017 Oct 10/3/2017; 18(Suppl 6): 690. PMID: 28984205, PMCID: PMC5629567, PII: 10.1186/s12864-017-4022-x, DOI: 10.1186/s12864-017-4022-x, ISSN: 1471-2164.
Zhao S, Samuels DC, Zhao YY, Guo Y. Tri-allelic heteroplasmies, DNA-RNA differences and their polynucleotide tract associations in the mitochondrial genome. Genomics [print-electronic]. 2017 Sep 9/29/2017; PMID: 28970049, PII: S0888-7543(17)30093-9, DOI: 10.1016/j.ygeno.2017.09.013, ISSN: 1089-8646.
Wang J, Samuels DC, Shyr Y, Guo Y. StrandScript: evaluation of Illumina genotyping array design and strand correction. Bioinformatics. 2017 Aug 8/1/2017; 33(15): 2399-401. PMID: 28402386, PII: 3204987, DOI: 10.1093/bioinformatics/btx186, ISSN: 1367-4811.
Zhang P, Lehmann BD, Samuels DC, Zhao S, Zhao YY, Shyr Y, Guo Y. Estimating relative mitochondrial DNA copy number using high throughput sequencing data. Genomics [print-electronic]. 2017 Jul 7/19/2017; PMID: 28734953, PII: S0888-7543(17)30060-5, DOI: 10.1016/j.ygeno.2017.07.002, ISSN: 1089-8646.
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, . Genome-wide association study of HIV-associated neurocognitive disorder (HAND): A CHARTER group study. Am. J. Med. Genet. B Neuropsychiatr. Genet [print-electronic]. 2017 Jun; 174(4): 413-26. PMID: 28447399, PMCID: PMC5435520, DOI: 10.1002/ajmg.b.32530, ISSN: 1552-485X.
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. Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults. Fluids Barriers CNS. 2017 Apr 4/21/2017; 14(1): 11. PMID: 28427421, PMCID: PMC5399327, PII: 10.1186/s12987-017-0058-1, DOI: 10.1186/s12987-017-0058-1, ISSN: 2045-8118.
Guo Y, Dai Y, Yu H, Zhao S, Samuels DC, Shyr Y. Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis. Genomics [print-electronic]. 2017 Mar; 109(2): 83-90. PMID: 28131802, PII: S0888-7543(17)30005-8, DOI: 10.1016/j.ygeno.2017.01.005, ISSN: 1089-8646.
Bregman JA, Herren DJ, Estopinal CB, Chocron IM, Harlow PA, Warden C, Brantley MA, Samuels DC. Mitochondrial Haplogroups Affect Severity But Not Prevalence of Diabetic Retinopathy. Invest. Ophthalmol. Vis. Sci. 2017 Feb 2/1/2017; 58(2): 1346-51. PMID: 28245487, PMCID: PMC5341621, PII: 2607959, DOI: 10.1167/iovs.16-20616, ISSN: 1552-5783.
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. OSBPL10, RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans. PLoS Pathog. 2017 Feb; 13(2): e1006220. PMID: 28241052, PMCID: PMC5344536, PII: PPATHOGENS-D-16-02742, DOI: 10.1371/journal.ppat.1006220, ISSN: 1553-7374.
Zhang P, Samuels DC, Zhao S, Wang J, Shyr Y, Guo Y. Practicability of mitochondrial heteroplasmy detection through an Illumina genotyping array. Mitochondrion [print-electronic]. 2016 Nov; 31: 75-8. PMID: 27628068, PII: S1567-7249(16)30061-7, DOI: 10.1016/j.mito.2016.08.018, ISSN: 1872-8278.
Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capra JA, Shyr Y, Zheng W, Guo Y. Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk. Genetics [print-electronic]. 2016 Nov; 204(3): 893-904. PMID: 27585849, PMCID: PMC5105867, PII: genetics.116.189936, DOI: 10.1534/genetics.116.189936, ISSN: 1943-2631.
Levinson RT, Hulgan T, Kalams SA, Fessel JP, Samuels DC. Mitochondrial Haplogroups as a Risk Factor for Herpes Zoster. Open Forum Infect Dis. 2016 Oct; 3(4): ofw184. PMID: 27807590, PMCID: PMC5088697, PII: ofw184, DOI: 10.1093/ofid/ofw184, ISSN: 2328-8957.
Samuels DC, Kallianpur AR, Ellis RJ, Bush WS, Letendre S, Franklin D, Grant I, Hulgan T. European Mitochondrial DNA Haplogroups are Associated with Cerebrospinal Fluid Biomarkers of Inflammation in HIV Infection. Pathog Immun. 2016 Sep; 1(2): 330-51. PMID: 28317034, PMCID: PMC5351881, DOI: 10.20411/pai.v1i2.156, ISSN: 2469-2964.
Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR. Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans. Cell Metab. 2016 Jul 7/12/2016; 24(1): 91-103. PMID: 27411011, PMCID: PMC5287496, PII: S1550-4131(16)30294-7, DOI: 10.1016/j.cmet.2016.06.008, ISSN: 1932-7420.
Zhang P, Samuels DC, Wang J, Zhao S, Shyr Y, Guo Y. Mitochondria single nucleotide variation across six blood cell types. Mitochondrion [print-electronic]. 2016 May; 28: 16-22. PMID: 26956645, PII: S1567-7249(16)30011-3, DOI: 10.1016/j.mito.2016.03.001, ISSN: 1872-8278.
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. Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck. Hum. Mol. Genet [print-electronic]. 2016 Mar 3/1/2016; 25(5): 1031-41. PMID: 26740552, PMCID: PMC4754047, PII: ddv626, DOI: 10.1093/hmg/ddv626, ISSN: 1460-2083.
Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L. Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs. Hum. Mutat [print-electronic]. 2015 Nov; 36(11): 1100-11. PMID: 26252938, DOI: 10.1002/humu.22849, ISSN: 1098-1004.
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, . Mitochondrial DNA Haplogroups and Neurocognitive Impairment During HIV Infection. Clin. Infect. Dis [print-electronic]. 2015 Nov 11/1/2015; 61(9): 1476-84. PMID: 26129753, PMCID: PMC4599391, PII: civ527, DOI: 10.1093/cid/civ527, ISSN: 1537-6591.
Wang J, Raskin L, Samuels DC, Shyr Y, Guo Y. Genome measures used for quality control are dependent on gene function and ancestry. Bioinformatics [print-electronic]. 2015 Feb 2/1/2015; 31(3): 318-23. PMID: 25297068, PMCID: PMC4308666, PII: btu668, DOI: 10.1093/bioinformatics/btu668, ISSN: 1367-4811.
Guo Y, Zhao S, Sheng Q, Guo M, Lehmann B, Pietenpol J, Samuels DC, Shyr Y. RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library. Biomed Res Int [print-electronic]. 2015; 2015: 862130. PMID: 26543871, PMCID: PMC4620295, DOI: 10.1155/2015/862130, ISSN: 2314-6141.
Guo Y, He J, Zhao S, Wu H, Zhong X, Sheng Q, Samuels DC, Shyr Y, Long J. Illumina human exome genotyping array clustering and quality control. Nat Protoc [print-electronic]. 2014 Nov; 9(11): 2643-62. PMID: 25321409, PMCID: PMC4441213, PII: nprot.2014.174, DOI: 10.1038/nprot.2014.174, ISSN: 1750-2799.
Estopinal CB, Chocron IM, Parks MB, Wade EA, Roberson RM, Burgess LG, Brantley MA, Samuels DC. Mitochondrial haplogroups are associated with severity of diabetic retinopathy. Invest. Ophthalmol. Vis. Sci. 2014 Sep; 55(9): 5589-95. PMID: 25118268, PMCID: PMC4160073, PII: iovs.14-15149, DOI: 10.1167/iovs.14-15149, ISSN: 1552-5783.
Ye F, Samuels DC, Clark T, Guo Y. High-throughput sequencing in mitochondrial DNA research. Mitochondrion [print-electronic]. 2014 Jul; 17: 157-63. PMID: 24859348, PMCID: PMC4149223, PII: S1567-7249(14)00078-6, DOI: 10.1016/j.mito.2014.05.004, ISSN: 1872-8278.
Eilertson B, Maruri F, Blackman A, Herrera M, Samuels DC, Sterling TR. High proportion of heteroresistance in gyrA and gyrB in fluoroquinolone-resistant Mycobacterium tuberculosis clinical isolates. Antimicrob. Agents Chemother [print-electronic]. 2014 Jun; 58(6): 3270-5. PMID: 24687490, PMCID: PMC4068501, PII: AAC.02066-13, DOI: 10.1128/AAC.02066-13, ISSN: 1098-6596.
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. Data from artificial models of mitochondrial DNA disorders are not always applicable to humans [letter]. Cell Rep. 2014 May 5/22/2014; 7(4): 933-4. PMID: 24856293, PII: S2211-1247(14)00380-5, DOI: 10.1016/j.celrep.2014.05.005, ISSN: 2211-1247.
Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann B, Pietenpol J, Samuels DC, Shyr Y. Multi-perspective quality control of Illumina exome sequencing data using QC3. Genomics [print-electronic]. 2014 May; 103(5-6): 323-8. PMID: 24703969, PII: S0888-7543(14)00035-4, DOI: 10.1016/j.ygeno.2014.03.006, ISSN: 1089-8646.
Pereira L, Soares P, Triska P, Rito T, van der Waerden A, Li B, Radivojac P, Samuels DC. Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential. Sci Rep. 2014; 4: 7155. PMID: 25412673, PMCID: PMC4239565, PII: srep07155, DOI: 10.1038/srep07155, ISSN: 2045-2322.
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, . Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy. PLoS ONE. 2014; 9(8): e103123. PMID: 25144566, PMCID: PMC4140681, PII: PONE-D-14-09650, DOI: 10.1371/journal.pone.0103123, ISSN: 1932-6203.
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. Recurrent tissue-specific mtDNA mutations are common in humans. PLoS Genet [print-electronic]. 2013 Nov; 9(11): e1003929. PMID: 24244193, PMCID: PMC3820769, PII: PGENETICS-D-13-01891, DOI: 10.1371/journal.pgen.1003929, ISSN: 1553-7404.
Hart AB, Samuels DC, Hulgan T. The other genome: a systematic review of studies of mitochondrial DNA haplogroups and outcomes of HIV infection and antiretroviral therapy. AIDS Rev. 2013 Oct; 15(4): 213-20. PMID: 24322381, PMCID: PMC4001077, ISSN: 1698-6997.
Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y. Finding the lost treasures in exome sequencing data. Trends Genet [print-electronic]. 2013 Oct; 29(10): 593-9. PMID: 23972387, PMCID: PMC3926691, PII: S0168-9525(13)00127-3, DOI: 10.1016/j.tig.2013.07.006, ISSN: 0168-9525.
Guo Y, Li J, Li CI, Shyr Y, Samuels DC. MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. Bioinformatics [print-electronic]. 2013 May 5/1/2013; 29(9): 1210-1. PMID: 23471301, PMCID: PMC4492415, PII: btt118, DOI: 10.1093/bioinformatics/btt118, ISSN: 1367-4811.
Samuels DC, Wonnapinij P, Chinnery PF. Preventing the transmission of pathogenic mitochondrial DNA mutations: Can we achieve long-term benefits from germ-line gene transfer?. Hum. Reprod [print-electronic]. 2013 Mar; 28(3): 554-9. PMID: 23297368, PMCID: PMC3571501, PII: des439, DOI: 10.1093/humrep/des439, ISSN: 1460-2350.
Guo Y, Sheng Q, Samuels DC, Lehmann B, Bauer JA, Pietenpol J, Shyr Y. Comparative study of exome copy number variation estimation tools using array comparative genomic hybridization as control. Biomed Res Int [print-electronic]. 2013; 2013: 915636. PMID: 24303503, PMCID: PMC3835197, DOI: 10.1155/2013/915636, ISSN: 2314-6141.
Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y. Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS ONE. 2013; 8(8): e71462. PMID: 23977046, PMCID: PMC3748065, PII: PONE-D-13-05180, DOI: 10.1371/journal.pone.0071462, ISSN: 1932-6203.
Guo Y, Samuels DC, Li J, Clark T, Li CI, Shyr Y. Evaluation of allele frequency estimation using pooled sequencing data simulation. ScientificWorldJournal [print-electronic]. 2013; 2013: 895496. PMID: 23476151, PMCID: PMC3582166, DOI: 10.1155/2013/895496, ISSN: 1537-744X.
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, . Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER. J. Neurovirol [print-electronic]. 2012 Dec; 18(6): 511-20. PMID: 23073667, PMCID: PMC3587171, DOI: 10.1007/s13365-012-0133-y, ISSN: 1538-2443.
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. Risk factors for symptomatic hyperlactatemia and lactic acidosis among combination antiretroviral therapy-treated adults in Botswana: results from a clinical trial. AIDS Res. Hum. Retroviruses [print-electronic]. 2012 Aug; 28(8): 759-65. PMID: 22540188, PMCID: PMC3399551, DOI: 10.1089/AID.2011.0303, ISSN: 1931-8405.
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. The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation. Mutat. Res [print-electronic]. 2012 May 5/15/2012; 744(2): 154-60. PMID: 22387842, PMCID: PMC3354959, PII: S1383-5718(12)00060-5, DOI: 10.1016/j.mrgentox.2012.02.006, ISSN: 0027-5107.
Pereira L, Soares P, Máximo V, Samuels DC. 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. BMC Cancer. 2012 Feb 2/2/2012; 12: 53. PMID: 22299657, PMCID: PMC3342922, PII: 1471-2407-12-53, DOI: 10.1186/1471-2407-12-53, ISSN: 1471-2407.
Chinnery PF, Elliott HR, Hudson G, Samuels DC, Relton CL. Epigenetics, epidemiology and mitochondrial DNA diseases. Int J Epidemiol [print-electronic]. 2012 Feb; 41(1): 177-87. PMID: 22287136, PMCID: PMC3304530, PII: dyr232, DOI: 10.1093/ije/dyr232, ISSN: 1464-3685.
Gandhi VV, Samuels DC. Correlated tissue expression of genes of cytoplasmic and mitochondrial nucleotide metabolisms in normal tissues is disrupted in transformed tissues. Nucleosides Nucleotides Nucleic Acids. 2012; 31(2): 112-29. PMID: 22303991, PMCID: PMC3464496, DOI: 10.1080/15257770.2011.644101, ISSN: 1532-2335.
Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y. The effect of strand bias in Illumina short-read sequencing data. BMC Genomics. 2012; 13: 666. PMID: 23176052, PMCID: PMC3532123, PII: 1471-2164-13-666, DOI: 10.1186/1471-2164-13-666, ISSN: 1471-2164.
Hulgan T, Robbins GK, Kalams SA, Samuels DC, Grady B, Shafer R, Murdock DG, Selph D, Haas DW, Pollard RB, . T cell activation markers and African mitochondrial DNA haplogroups among non-Hispanic black participants in AIDS clinical trials group study 384. PLoS ONE [print-electronic]. 2012; 7(8): e43803. PMID: 22970105, PMCID: PMC3433792, PII: PONE-D-12-11386, DOI: 10.1371/journal.pone.0043803, ISSN: 1932-6203.
Grady BJ, Samuels DC, Robbins GK, Selph D, Canter JA, Pollard RB, Haas DW, Shafer R, Kalams SA, Murdock DG, Ritchie MD, Hulgan T, . Mitochondrial genomics and CD4 T-cell count recovery after antiretroviral therapy initiation in AIDS clinical trials group study 384. J. Acquir. Immune Defic. Syndr. 2011 Dec 12/1/2011; 58(4): 363-70. PMID: 21792066, PMCID: PMC3204178, DOI: 10.1097/QAI.0b013e31822c688b, ISSN: 1944-7884.
Song Z, Cao Y, Samuels DC. Replication pauses of the wild-type and mutant mitochondrial DNA polymerase gamma: a simulation study. PLoS Comput. Biol [print-electronic]. 2011 Nov; 7(11): e1002287. PMID: 22125488, PMCID: PMC3219627, PII: PCOMPBIOL-D-11-00627, DOI: 10.1371/journal.pcbi.1002287, ISSN: 1553-7358.
Gandhi VV, Samuels DC. Enzyme kinetics of the mitochondrial deoxyribonucleoside salvage pathway are not sufficient to support rapid mtDNA replication. PLoS Comput. Biol [print-electronic]. 2011 Aug; 7(8): e1002078. PMID: 21829339, PMCID: PMC3150320, PII: PCOMPBIOL-D-11-00157, DOI: 10.1371/journal.pcbi.1002078, ISSN: 1553-7358.
Gandhi VV, Samuels DC. A review comparing deoxyribonucleoside triphosphate (dNTP) concentrations in the mitochondrial and cytoplasmic compartments of normal and transformed cells. Nucleosides Nucleotides Nucleic Acids. 2011 May; 30(5): 317-39. PMID: 21774628, PMCID: PMC3210641, DOI: 10.1080/15257770.2011.586955, ISSN: 1532-2335.
Howells CC, Baumann WT, Samuels DC, Finkielstein CV. The Bcl-2-associated death promoter (BAD) lowers the threshold at which the Bcl-2-interacting domain death agonist (BID) triggers mitochondria disintegration. J. Theor. Biol [print-electronic]. 2011 Feb 2/21/2011; 271(1): 114-23. PMID: 21130780, PII: S0022-5193(10)00635-1, DOI: 10.1016/j.jtbi.2010.11.040, ISSN: 1095-8541.
Yu-Wai-Man P, Sitarz KS, Samuels DC, Griffiths PG, Reeve AK, Bindoff LA, Horvath R, Chinnery PF. OPA1 mutations cause cytochrome c oxidase deficiency due to loss of wild-type mtDNA molecules. Hum. Mol. Genet [print-electronic]. 2010 Aug 8/1/2010; 19(15): 3043-52. PMID: 20484224, PMCID: PMC2901142, PII: ddq209, DOI: 10.1093/hmg/ddq209, ISSN: 1460-2083.
Song Z, Samuels DC. Analysis of enzyme kinetic data for mtDNA replication. Methods [print-electronic]. 2010 Aug; 51(4): 385-91. PMID: 20188839, PMCID: PMC2903644, PII: S1046-2023(10)00095-2, DOI: 10.1016/j.ymeth.2010.02.019, ISSN: 1095-9130.
Samuels DC, Wonnapinij P, Cree LM, Chinnery PF. Reassessing evidence for a postnatal mitochondrial genetic bottleneck [letter]. Nat. Genet. 2010 Jun; 42(6): 471-2; author reply 472. PMID: 20502486, PII: ng0610-471, DOI: 10.1038/ng0610-471, ISSN: 1546-1718.
Wonnapinij P, Chinnery PF, Samuels DC. Previous estimates of mitochondrial DNA mutation level variance did not account for sampling error: comparing the mtDNA genetic bottleneck in mice and humans. Am. J. Hum. Genet [print-electronic]. 2010 Apr 4/9/2010; 86(4): 540-50. PMID: 20362273, PMCID: PMC2850432, PII: S0002-9297(10)00139-4, DOI: 10.1016/j.ajhg.2010.02.023, ISSN: 1537-6605.
Marchington D, Malik S, Banerjee A, Turner K, Samuels D, Macaulay V, Oakeshott P, Fratter C, Kennedy S, Poulton J. Information for genetic management of mtDNA disease: sampling pathogenic mtDNA mutants in the human germline and in placenta. J. Med. Genet [print-electronic]. 2010 Apr; 47(4): 257-61. PMID: 19914907, PII: jmg.2009.072900, DOI: 10.1136/jmg.2009.072900, ISSN: 1468-6244.
Cree LM, Samuels DC, Chinnery PF. The inheritance of pathogenic mitochondrial DNA mutations. Biochim. Biophys. Acta [print-electronic]. 2009 Dec; 1792(12): 1097-102. PMID: 19303927, PMCID: PMC2785871, PII: S0925-4439(09)00062-3, DOI: 10.1016/j.bbadis.2009.03.002, ISSN: 0006-3002.
Samuels DC, Burn DJ, Chinnery PF. Detecting new neurodegenerative disease genes: does phenotype accuracy limit the horizon? [letter]. Trends Genet [print-electronic]. 2009 Nov; 25(11): 486-8. PMID: 19819581, PMCID: PMC2824109, PII: S0168-9525(09)00181-4, DOI: 10.1016/j.tig.2009.09.008, ISSN: 0168-9525.
Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, Costa S, Máximo V, Macaulay V, Rocha R, Samuels DC. The diversity present in 5140 human mitochondrial genomes. Am. J. Hum. Genet [print-electronic]. 2009 May; 84(5): 628-40. PMID: 19426953, PMCID: PMC2681004, PII: S0002-9297(09)00155-4, DOI: 10.1016/j.ajhg.2009.04.013, ISSN: 1537-6605.
Guan X, Silva P, Gyenai KB, Xu J, Geng T, Tu Z, Samuels DC, Smith EJ. The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo. Anim. Genet [print-electronic]. 2009 Apr; 40(2): 134-41. PMID: 19067672, PMCID: PMC2664387, PII: AGE1810, DOI: 10.1111/j.1365-2052.2008.01810.x, ISSN: 1365-2052.
Cao Y, Samuels DC. Discrete stochastic simulation methods for chemically reacting systems. Meth. Enzymol. 2009; 454: 115-40. PMID: 19216925, PMCID: PMC3492891, PII: S0076-6879(08)03805-6, DOI: 10.1016/S0076-6879(08)03805-6, ISSN: 1557-7988.
Wendelsdorf KV, Song Z, Cao Y, Samuels DC. An analysis of enzyme kinetics data for mitochondrial DNA strand termination by nucleoside reverse transcription inhibitors. PLoS Comput. Biol [print-electronic]. 2009 Jan; 5(1): e1000261. PMID: 19132079, PMCID: PMC2603287, DOI: 10.1371/journal.pcbi.1000261, ISSN: 1553-7358.
Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, Amorim A. Evidence for variable selective pressures at a large secondary structure of the human mitochondrial DNA control region. Mol. Biol. Evol [print-electronic]. 2008 Dec; 25(12): 2759-70. PMID: 18845547, PII: msn225, DOI: 10.1093/molbev/msn225, ISSN: 1537-1719.
Wonnapinij P, Chinnery PF, Samuels DC. The distribution of mitochondrial DNA heteroplasmy due to random genetic drift. Am. J. Hum. Genet [print-electronic]. 2008 Nov; 83(5): 582-93. PMID: 18976726, PMCID: PMC2668051, PII: S0002-9297(08)00542-9, DOI: 10.1016/j.ajhg.2008.10.007, ISSN: 1537-6605.
Elliott HR, Samuels DC, Eden JA, Relton CL, Chinnery PF. Pathogenic mitochondrial DNA mutations are common in the general population. Am. J. Hum. Genet. 2008 Aug; 83(2): 254-60. PMID: 18674747, PMCID: PMC2495064, PII: S0002-9297(08)00402-3, DOI: 10.1016/j.ajhg.2008.07.004, ISSN: 1537-6605.
Krishnan KJ, Reeve AK, Samuels DC, Chinnery PF, Blackwood JK, Taylor RW, Wanrooij S, Spelbrink JN, Lightowlers RN, Turnbull DM. What causes mitochondrial DNA deletions in human cells?. Nat. Genet. 2008 Mar; 40(3): 275-9. PMID: 18305478, PII: ng.f.94, DOI: 10.1038/ng.f.94, ISSN: 1546-1718.
Kang J, Samuels DC. The evidence that the DNC (SLC25A19) is not the mitochondrial deoxyribonucleotide carrier. Mitochondrion [print-electronic]. 2008 Mar; 8(2): 103-8. PMID: 18280798, PII: S1567-7249(08)00002-0, DOI: 10.1016/j.mito.2008.01.001, ISSN: 1567-7249.
Rajasimha HK, Chinnery PF, Samuels DC. Selection against pathogenic mtDNA mutations in a stem cell population leads to the loss of the 3243A-->G mutation in blood. Am. J. Hum. Genet. 2008 Feb; 82(2): 333-43. PMID: 18252214, PMCID: PMC2427290, PII: S0002-9297(08)00085-2, DOI: 10.1016/j.ajhg.2007.10.007, ISSN: 1537-6605.
Cree LM, Samuels DC, de Sousa Lopes SC, Rajasimha HK, Wonnapinij P, Mann JR, Dahl HH, Chinnery PF. A reduction of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes. Nat. Genet [print-electronic]. 2008 Feb; 40(2): 249-54. PMID: 18223651, PII: ng.2007.63, DOI: 10.1038/ng.2007.63, ISSN: 1546-1718.
Durham SE, Samuels DC, Cree LM, Chinnery PF. Normal levels of wild-type mitochondrial DNA maintain cytochrome c oxidase activity for two pathogenic mitochondrial DNA mutations but not for m.3243A-->G. Am. J. Hum. Genet [print-electronic]. 2007 Jul; 81(1): 189-95. PMID: 17564976, PMCID: PMC1950909, PII: S0002-9297(07)62829-8, DOI: 10.1086/518901, ISSN: 0002-9297.
Samuels DC. Computational models of antiviral toxicity. Curr Opin Drug Discov Devel. 2007 Jan; 10(1): 43-8. PMID: 17265740, ISSN: 1367-6733.
Pyle A, Taylor RW, Durham SE, Deschauer M, Schaefer AM, Samuels DC, Chinnery PF. Depletion of mitochondrial DNA in leucocytes harbouring the 3243A->G mtDNA mutation [letter]. J. Med. Genet [print-electronic]. 2007 Jan; 44(1): 69-74. PMID: 16950816, PMCID: PMC2597915, PII: jmg.2006.043109, DOI: 10.1136/jmg.2006.043109, ISSN: 1468-6244.
Samuels DC. Mitochondrial AZT metabolism. IUBMB Life. 2006 Jul; 58(7): 403-8. PMID: 16801215, PII: K032UV7JUK7V3618, DOI: 10.1080/15216540600791571, ISSN: 1521-6543.
Durham SE, Samuels DC, Chinnery PF. Is selection required for the accumulation of somatic mitochondrial DNA mutations in post-mitotic cells?. Neuromuscul. Disord [print-electronic]. 2006 Jun; 16(6): 381-6. PMID: 16684599, PII: S0960-8966(06)00093-9, DOI: 10.1016/j.nmd.2006.03.012, ISSN: 0960-8966.
Samuels DC, Carothers AD, Horton R, Chinnery PF. The power to detect disease associations with mitochondrial DNA haplogroups. Am. J. Hum. Genet [print-electronic]. 2006 Apr; 78(4): 713-20. PMID: 16532401, PMCID: PMC1424681, PII: S0002-9297(07)63709-4, DOI: 10.1086/502682, ISSN: 0002-9297.
Bradshaw PC, Li J, Samuels DC. A computational model of mitochondrial AZT metabolism. Biochem. J. 2005 Dec 12/1/2005; 392(Pt 2): 363-73. PMID: 16060859, PMCID: PMC1316272, PII: BJ20050749, DOI: 10.1042/BJ20050749, ISSN: 1470-8728.
Samuels DC. Life span is related to the free energy of mitochondrial DNA. Mech. Ageing Dev. 2005 Oct; 126(10): 1123-9. PMID: 15992863, PII: S0047-6374(05)00120-X, DOI: 10.1016/j.mad.2005.05.003, ISSN: 0047-6374.
Durham SE, Bonilla E, Samuels DC, DiMauro S, Chinnery PF. Mitochondrial DNA copy number threshold in mtDNA depletion myopathy. Neurology. 2005 Aug 8/9/2005; 65(3): 453-5. PMID: 16087914, PII: 65/3/453, DOI: 10.1212/01.wnl.0000171861.30277.88, ISSN: 1526-632X.
Bradshaw PC, Samuels DC. A computational model of mitochondrial deoxynucleotide metabolism and DNA replication. Am. J. Physiol., Cell Physiol [print-electronic]. 2005 May; 288(5): C989-1002. PMID: 15634740, PII: 00530.2004, DOI: 10.1152/ajpcell.00530.2004, ISSN: 0363-6143.
Bradshaw PC, Rathi A, Samuels DC. Mitochondrial-encoded membrane protein transcripts are pyrimidine-rich while soluble protein transcripts and ribosomal RNA are purine-rich. BMC Genomics. 2005; 6: 136. PMID: 16185363, PMCID: PMC1262711, PII: 1471-2164-6-136, DOI: 10.1186/1471-2164-6-136, ISSN: 1471-2164.
Samuels DC, Schon EA, Chinnery PF. Two direct repeats cause most human mtDNA deletions. Trends Genet. 2004 Sep; 20(9): 393-8. PMID: 15313545, PII: S0168-9525(04)00183-0, DOI: 10.1016/j.tig.2004.07.003, ISSN: 0168-9525.
Samuels DC. Mitochondrial DNA repeats constrain the life span of mammals. Trends Genet. 2004 May; 20(5): 226-9. PMID: 15109774, PII: S0168-9525(04)00071-X, DOI: 10.1016/j.tig.2004.03.003, ISSN: 0168-9525.
Taylor RW, Barron MJ, Borthwick GM, Gospel A, Chinnery PF, Samuels DC, Taylor GA, Plusa SM, Needham SJ, Greaves LC, Kirkwood TB, Turnbull DM. Mitochondrial DNA mutations in human colonic crypt stem cells. J. Clin. Invest. 2003 Nov; 112(9): 1351-60. PMID: 14597761, PMCID: PMC228466, PII: 112/9/1351, DOI: 10.1172/JCI19435, ISSN: 0021-9738.
Samuels DC, Boys RJ, Henderson DA, Chinnery PF. A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate. Nucleic Acids Res. 2003 Oct 10/15/2003; 31(20): 6043-52. PMID: 14530452, PMCID: PMC219467, ISSN: 1362-4962.
Capps GJ, Samuels DC, Chinnery PF. A model of the nuclear control of mitochondrial DNA replication. J. Theor. Biol. 2003 Apr 4/21/2003; 221(4): 565-83. PMID: 12713941, PII: S0022519303932073, ISSN: 0022-5193.
Barenghi CF, Hulton S, Samuels DC. Polarization of superfluid turbulence. Phys. Rev. Lett [print-electronic]. 2002 Dec 12/30/2002; 89(27): 275301. PMID: 12513214, DOI: 10.1103/PhysRevLett.89.275301, ISSN: 0031-9007.
Elson JL, Samuels DC, Johnson MA, Turnbull DM, Chinnery PF. The length of cytochrome c oxidase-negative segments in muscle fibres in patients with mtDNA myopathy. Neuromuscul. Disord. 2002 Nov; 12(9): 858-64. PMID: 12398838, PII: S0960896602000470, ISSN: 0960-8966.
Chinnery PF, Samuels DC, Elson J, Turnbull DM. Accumulation of mitochondrial DNA mutations in ageing, cancer, and mitochondrial disease: is there a common mechanism?. Lancet. 2002 Oct 10/26/2002; 360(9342): 1323-5. PMID: 12414225, PII: S0140-6736(02)11310-9, DOI: 10.1016/S0140-6736(02)11310-9, ISSN: 0140-6736.
Barenghi CF, Samuels DC. Evaporation of a packet of quantized vorticity. Phys. Rev. Lett [print-electronic]. 2002 Oct 10/7/2002; 89(15): 155302. PMID: 12365997, DOI: 10.1103/PhysRevLett.89.155302, ISSN: 0031-9007.
Kivotides D, Vassilicos JC, Barenghi CF, Khan MA, Samuels DC. Quantum signature of superfluid turbulence. Phys. Rev. Lett [print-electronic]. 2001 Dec 12/31/2001; 87(27 Pt 1): 275302. PMID: 11800889, DOI: 10.1103/PhysRevLett.87.275302, ISSN: 0031-9007.
Kivotides D, Barenghi CF, Samuels DC. Fractal dimension of superfluid turbulence. Phys. Rev. Lett [print-electronic]. 2001 Oct 10/8/2001; 87(15): 155301. PMID: 11580706, DOI: 10.1103/PhysRevLett.87.155301, ISSN: 0031-9007.
Kivotides D, Vassilicos JC, Samuels DC, Barenghi CF. Kelvin waves cascade in superfluid turbulence. Phys. Rev. Lett. 2001 Apr 4/2/2001; 86(14): 3080-3. PMID: 11290112, DOI: 10.1103/PhysRevLett.86.3080, ISSN: 0031-9007.
Elson JL, Samuels DC, Turnbull DM, Chinnery PF. Random intracellular drift explains the clonal expansion of mitochondrial DNA mutations with age. Am. J. Hum. Genet [print-electronic]. 2001 Mar; 68(3): 802-6. PMID: 11179029, PMCID: PMC1274494, PII: S0002-9297(07)63121-8, DOI: 10.1086/318801, ISSN: 0002-9297.
Leadbeater M, Winiecki T, Samuels DC, Barenghi CF, Adams CS. Sound emission due to superfluid vortex reconnections. Phys. Rev. Lett. 2001 Feb 2/19/2001; 86(8): 1410-3. PMID: 11290155, DOI: 10.1103/PhysRevLett.86.1410, ISSN: 0031-9007.
Brown DT, Samuels DC, Michael EM, Turnbull DM, Chinnery PF. Random genetic drift determines the level of mutant mtDNA in human primary oocytes. Am. J. Hum. Genet [print-electronic]. 2001 Feb; 68(2): 533-6. PMID: 11133360, PMCID: PMC1235288, PII: S0002-9297(07)64107-X, DOI: 10.1086/318190, ISSN: 0002-9297.
Chinnery PF, Thorburn DR, Samuels DC, White SL, Dahl HM, Turnbull DM, Lightowlers RN, Howell N. The inheritance of mitochondrial DNA heteroplasmy: random drift, selection or both?. Trends Genet. 2000 Nov; 16(11): 500-5. PMID: 11074292, PII: S016895250002120X, ISSN: 0168-9525.
Kivotides D, Barenghi CF, Samuels DC. Triple vortex ring structure in superfluid helium II. Science. 2000 Oct 10/27/2000; 290(5492): 777-9. PMID: 11052935, PII: 8937, ISSN: 0036-8075.
Chinnery PF, Samuels DC. Relaxed replication of mtDNA: A model with implications for the expression of disease. Am. J. Hum. Genet. 1999 Apr; 64(4): 1158-65. PMID: 10090901, PMCID: PMC1377840, PII: AJHG980454, ISSN: 0002-9297.
Miller KE, Samuels DC. The axon as a metabolic compartment: protein degradation, transport, and maximum length of an axon. J. Theor. Biol. 1997 Jun 6/7/1997; 186(3): 373-9. PMID: 9219672, PII: S0022-5193(96)90355-0, DOI: 10.1006/jtbi.1996.0355, ISSN: 0022-5193.
Samuels DC, Hentschel HG, Fine A. The origin of neuronal polarization: a model of axon formation. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 1996 Sep 9/30/1996; 351(1344): 1147-56. PMID: 8899865, DOI: 10.1098/rstb.1996.0099, ISSN: 0962-8436.
Samuels DC. Response of superfluid vortex filaments to concentrated normal-fluid vorticity. Phys. Rev., B Condens. Matter. 1993 Jan 1/1/1993; 47(2): 1107-10. PMID: 10005596, ISSN: 0163-1829.
Samuels DC. Velocity matching and Poiseuille pipe flow of superfluid helium. Phys. Rev., B Condens. Matter. 1992 Nov 11/1/1992; 46(18): 11714-24. PMID: 10003062, ISSN: 0163-1829.
Samuels DC, Donnelly RJ. Motion of charged vortex rings in helium II. Phys. Rev. Lett. 1991 Oct 10/28/1991; 67(18): 2505-8. PMID: 10044443, DOI: 10.1103/PhysRevLett.67.2505, ISSN: 1079-7114.
Samuels DC, Donnelly RJ. Dynamics of the interactions of rotons with quantized vortices in helium II. Phys. Rev. Lett. 1990 Jul 7/9/1990; 65(2): 187-90. PMID: 10042575, DOI: 10.1103/PhysRevLett.65.187, ISSN: 1079-7114.
Samuels DC, Donnelly RJ. Sideband instability and recurrence of Kelvin waves on vortex cores. Phys. Rev. Lett. 1990 Mar 3/19/1990; 64(12): 1385-8. PMID: 10041382, DOI: 10.1103/PhysRevLett.64.1385, ISSN: 1079-7114.