David C. Samuels - Publications

Molecular Physiology and Biophysics Vanderbilt University Medical School 

127 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Samuels DC, Hulgan T, Fessel JP, Billings FT, Thompson JL, Chandrasekhar R, Girard TD. Mitochondrial DNA Haplogroups and Delirium During Sepsis. Critical Care Medicine. 47: 1065-1071. PMID 31306254 DOI: 10.1097/CCM.0000000000003810  1
2019 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. Frontiers in Genetics. 10: 211. PMID 30949194 DOI: 10.3389/fgene.2019.00211  1
2019 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, et al. Identification of serum metabolites associating with chronic kidney disease progression and anti-fibrotic effect of 5-methoxytryptophan. Nature Communications. 10: 1476. PMID 30931940 DOI: 10.1038/s41467-019-09329-0  1
2019 Yu H, Samuels DC, Zhao YY, Guo Y. Architectures and accuracy of artificial neural network for disease classification from omics data. Bmc Genomics. 20: 167. PMID 30832569 DOI: 10.1186/s12864-019-5546-z  1
2018 Guo Y, Yu H, Samuels DC, Yue W, Ness S, Zhao YY. Corrigendum to: Single-nucleotide variants in human RNA: RNA editing and beyond. Briefings in Functional Genomics. PMID 30596888 DOI: 10.1093/bfgp/ely041  1
2018 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. Journal of Acquired Immune Deficiency Syndromes (1999). PMID 30531306 DOI: 10.1097/QAI.0000000000001930  1
2018 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. Journal of Acquired Immune Deficiency Syndromes (1999). PMID 30531304 DOI: 10.1097/QAI.0000000000001926  1
2018 Sheng Q, Samuels DC, Yu H, Ness S, Zhao YY, Guo Y. Cancer-specific expression quantitative loci are affected by expression dysregulation. Briefings in Bioinformatics. PMID 30475999 DOI: 10.1093/bib/bby108  1
2018 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 Medical Genomics. 11: 105. PMID 30453947 DOI: 10.1186/s12920-018-0416-0  1
2018 Guo Y, Yu H, Samuels DC, Yue W, Ness S, Zhao YY. Single-nucleotide variants in human RNA: RNA editing and beyond. Briefings in Functional Genomics. PMID 30312373 DOI: 10.1093/bfgp/ely032  1
2018 Kallianpur AR, Gerschenson M, Hulgan T, Kaur H, Clifford D, Haas D, Murdock DG, McArthur JC, Samuels DC, Simpson D. Hemochromatosis (HFE) Gene Variants are Associated with Increased Mitochondrial DNA Levels during HIV-1 Infection and Antiretroviral Therapy. Aids Research and Human Retroviruses. PMID 29968489 DOI: 10.1089/AID.2018.0025  1
2018 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. The American Journal of Cardiology. PMID 29914646 DOI: 10.1016/j.amjcard.2018.04.011  0.01
2018 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. PMID 29902512 DOI: 10.1016/j.ygeno.2018.06.001  1
2018 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. Human Reproduction (Oxford, England). PMID 29850888 DOI: 10.1093/humrep/dey114  1
2018 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. PMID 29631022 DOI: 10.1016/j.mito.2018.04.001  1
2018 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 HIV. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 29481608 DOI: 10.1093/cid/ciy151  1
2017 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. Investigative Ophthalmology & Visual Science. 58: 6481-6488. PMID 29288266 DOI: 10.1167/iovs.17-22804  1
2017 Wang J, Samuels DC, Zhao S, Xiang Y, Zhao YY, Guo Y. Current Research on Non-Coding Ribonucleic Acid (RNA). Genes. 8. PMID 29206165 DOI: 10.3390/genes8120366  1
2017 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. 18: 690. PMID 28984205 DOI: 10.1186/s12864-017-4022-x  1
2017 Zhao S, Samuels DC, Zhao YY, Guo Y. Tri-allelic heteroplasmies, DNA-RNA differences and their polynucleotide tract associations in the mitochondrial genome. Genomics. PMID 28970049 DOI: 10.1016/j.ygeno.2017.09.013  1
2017 Guo Y, Sheng Q, Samuels DC, Lehmann B, Bauer JA, Pietenpol J, Shyr Y. Corrigendum to "Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control". Biomed Research International. 2017: 7409598. PMID 28804721 DOI: 10.1155/2017/7409598  1
2017 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. PMID 28734953 DOI: 10.1016/j.ygeno.2017.07.002  1
2017 Li CI, Samuels DC, Zhao YY, Shyr Y, Guo Y. Power and sample size calculations for high-throughput sequencing-based experiments. Briefings in Bioinformatics. PMID 28605403 DOI: 10.1093/bib/bbx061  1
2017 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, et al. Genome-wide association study of HIV-associated neurocognitive disorder (HAND): A CHARTER group study. American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics. PMID 28447399 DOI: 10.1002/ajmg.b.32530  1
2017 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 and Barriers of the Cns. 14: 11. PMID 28427421 DOI: 10.1186/s12987-017-0058-1  1
2017 Wang J, Samuels DC, Shyr Y, Guo Y. StrandScript: Evaluation of Illumina Genotyping Array Design and Strand Correction. Bioinformatics (Oxford, England). PMID 28402386 DOI: 10.1093/bioinformatics/btx186  1
2017 Zhao S, Jing W, Samuels DC, Sheng Q, Shyr Y, Guo Y. Strategies for processing and quality control of Illumina genotyping arrays. Briefings in Bioinformatics. PMID 28334151 DOI: 10.1093/bib/bbx012  1
2017 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. Investigative Ophthalmology & Visual Science. 58: 1346-1351. PMID 28245487 DOI: 10.1167/iovs.16-20616  1
2017 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 Pathogens. 13: e1006220. PMID 28241052 DOI: 10.1371/journal.ppat.1006220  1
2017 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. PMID 28131802 DOI: 10.1016/j.ygeno.2017.01.005  1
2016 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. Pathogens & Immunity. 1: 330-351. PMID 28317034 DOI: 10.20411/pai.v1i2.156  1
2016 Wiley LK, Vanhouten JP, Samuels DC, Aldrich MC, Roden DM, Peterson JF, Denny JC. STRATEGIES FOR EQUITABLE PHARMACOGENOMIC-GUIDED WARFARIN DOSING AMONG EUROPEAN AND AFRICAN AMERICAN INDIVIDUALS IN A CLINICAL POPULATION. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 22: 545-556. PMID 27897005  0.01
2016 Levinson RT, Hulgan T, Kalams SA, Fessel JP, Samuels DC. Mitochondrial Haplogroups as a Risk Factor for Herpes Zoster. Open Forum Infectious Diseases. 3: ofw184. PMID 27807590 DOI: 10.1093/ofid/ofw184  1
2016 Sheng Q, Vickers K, Zhao S, Wang J, Samuels DC, Koues O, Shyr Y, Guo Y. Multi-perspective quality control of Illumina RNA sequencing data analysis. Briefings in Functional Genomics. PMID 27687708 DOI: 10.1093/bfgp/elw035  1
2016 Zhang P, Samuels DC, Zhao S, Wang J, Shyr Y, Guo Y. Practicability of Mitochondrial Heteroplasmy Detection through an Illumina Genotyping Array. Mitochondrion. PMID 27628068 DOI: 10.1016/j.mito.2016.08.018  1
2016 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. PMID 27585849 DOI: 10.1534/genetics.116.189936  1
2016 Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR. Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans. Cell Metabolism. 24: 91-103. PMID 27411011 DOI: 10.1016/j.cmet.2016.06.008  0.01
2016 Zhang P, Samuels DC, Wang J, Zhao S, Shyr Y, Guo Y. Mitochondria single nucleotide variation across six blood cell types. Mitochondrion. PMID 26956645 DOI: 10.1016/j.mito.2016.03.001  1
2016 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, et al. Mitochondrial DNA Sequence Characteristics Modulate the Size of the Genetic Bottleneck. Human Molecular Genetics. PMID 26740552 DOI: 10.1093/hmg/ddv626  1
2015 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 Research International. 2015: 862130. PMID 26543871 DOI: 10.1155/2015/862130  1
2015 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. Human Mutation. 36: 1100-11. PMID 26252938 DOI: 10.1002/humu.22849  1
2015 Zhang P, Samuels DC, Lehmann B, Stricker T, Pietenpol J, Shyr Y, Guo Y. Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data. Briefings in Bioinformatics. PMID 26249222 DOI: 10.1093/bib/bbv057  1
2015 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, et al. Mitochondrial DNA Haplogroups and Neurocognitive Impairment during HIV Infection. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 26129753 DOI: 10.1093/cid/civ527  1
2015 Wang J, Raskin L, Samuels DC, Shyr Y, Guo Y. Genome measures used for quality control are dependent on gene function and ancestry. Bioinformatics (Oxford, England). 31: 318-23. PMID 25297068 DOI: 10.1093/bioinformatics/btu668  1
2015 Han L, Vickers KC, Samuels DC, Guo Y. Alternative applications for distinct RNA sequencing strategies. Briefings in Bioinformatics. 16: 629-39. PMID 25246237 DOI: 10.1093/bib/bbu032  1
2014 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. Scientific Reports. 4: 7155. PMID 25412673 DOI: 10.1038/srep07155  1
2014 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. Nature Protocols. 9: 2643-62. PMID 25321409 DOI: 10.1038/nprot.2014.174  1
2014 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, ... ... Samuels DC, et al. Genetic variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy. Plos One. 9: e103123. PMID 25144566 DOI: 10.1371/journal.pone.0103123  1
2014 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. Investigative Ophthalmology & Visual Science. 55: 5589-95. PMID 25118268 DOI: 10.1167/iovs.14-15149  1
2014 Ye F, Samuels DC, Clark T, Guo Y. High-throughput sequencing in mitochondrial DNA research. Mitochondrion. 17: 157-63. PMID 24859348 DOI: 10.1016/j.mito.2014.05.004  1
2014 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. Cell Reports. 7: 933-4. PMID 24856293 DOI: 10.1016/j.celrep.2014.05.005  1
2014 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, et al. Epidermal nerve fiber density, oxidative stress, and mitochondrial haplogroups in HIV-infected Thais initiating therapy. Aids (London, England). 28: 1625-33. PMID 24785954 DOI: 10.1097/QAD.0000000000000297  1
2014 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. 103: 323-8. PMID 24703969 DOI: 10.1016/j.ygeno.2014.03.006  1
2014 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. Antimicrobial Agents and Chemotherapy. 58: 3270-5. PMID 24687490 DOI: 10.1128/AAC.02066-13  1
2014 Damas J, Samuels DC, Carneiro J, Amorim A, Pereira F. Mitochondrial DNA rearrangements in health and disease--a comprehensive study. Human Mutation. 35: 1-14. PMID 24115352 DOI: 10.1002/humu.22452  1
2014 Guo Y, Ye F, Sheng Q, Clark T, Samuels DC. Three-stage quality control strategies for DNA re-sequencing data. Briefings in Bioinformatics. 15: 879-89. PMID 24067931 DOI: 10.1093/bib/bbt069  1
2013 Pu Y, Lee S, Samuels DC, Watson LT, Cao Y. The effect of unhealthy β-cells on insulin secretion in pancreatic islets. Bmc Medical Genomics. 6: S6. PMID 24565418 DOI: 10.1186/1755-8794-6-S3-S6  1
2013 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 Reviews. 15: 213-20. PMID 24322381  1
2013 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 Research International. 2013: 915636. PMID 24303503 DOI: 10.1155/2013/915636  1
2013 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 Genetics. 9: e1003929. PMID 24244193 DOI: 10.1371/journal.pgen.1003929  1
2013 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. 8: e71462. PMID 23977046 DOI: 10.1371/journal.pone.0071462  1
2013 Samuels DC, Han L, Li J, Quanghu S, Clark TA, Shyr Y, Guo Y. Finding the lost treasures in exome sequencing data. Trends in Genetics : Tig. 29: 593-9. PMID 23972387 DOI: 10.1016/j.tig.2013.07.006  1
2013 Soares P, Abrantes D, Rito T, Thomson N, Radivojac P, Li B, Macaulay V, Samuels DC, Pereira L. Evaluating purifying selection in the mitochondrial DNA of various mammalian species. Plos One. 8: e58993. PMID 23533597 DOI: 10.1371/journal.pone.0058993  1
2013 Guo Y, Samuels DC, Li J, Clark T, Li CI, Shyr Y. Evaluation of allele frequency estimation using pooled sequencing data simulation. Thescientificworldjournal. 2013: 895496. PMID 23476151 DOI: 10.1155/2013/895496  1
2013 Guo Y, Li J, Li CI, Shyr Y, Samuels DC. MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis. Bioinformatics (Oxford, England). 29: 1210-1. PMID 23471301 DOI: 10.1093/bioinformatics/btt118  1
2013 Sinxadi PZ, Dave JA, Samuels DC, Heckmann JM, Maartens G, Levitt NS, Wester CW, Haas DW, Hulgan T. Mitochondrial genomics and antiretroviral therapy-associated metabolic complications in HIV-infected Black South Africans: a pilot study. Aids Research and Human Retroviruses. 29: 1031-9. PMID 23428049 DOI: 10.1089/AID.2012.0373  1
2013 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. Mutation dependance of the mitochondrial DNA copy number in the first stages of human embryogenesis. Human Molecular Genetics. 22: 1867-72. PMID 23390135 DOI: 10.1093/hmg/ddt040  1
2013 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? Human Reproduction (Oxford, England). 28: 554-9. PMID 23297368 DOI: 10.1093/humrep/des439  1
2013 Payne BA, Wilson IJ, Yu-Wai-Man P, Coxhead J, Deehan D, Horvath R, Taylor RW, Samuels DC, Santibanez-Koref M, Chinnery PF. Universal heteroplasmy of human mitochondrial DNA. Human Molecular Genetics. 22: 384-90. PMID 23077218 DOI: 10.1093/hmg/dds435  1
2013 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, ... ... Samuels DC, et al. No evidence of an association between mitochondrial DNA variants and osteoarthritis in 7393 cases and 5122 controls. Annals of the Rheumatic Diseases. 72: 136-9. PMID 22984172 DOI: 10.1136/annrheumdis-2012-201932  1
2012 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. Non-random mtDNA segregation patterns indicate a metastable heteroplasmic segregation unit in m.3243A>G cybrid cells. Plos One. 7: e52080. PMID 23272214 DOI: 10.1371/journal.pone.0052080  1
2012 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, et al. What is influencing the phenotype of the common homozygous polymerase-γ mutation p.Ala467Thr? Brain : a Journal of Neurology. 135: 3614-26. PMID 23250882 DOI: 10.1093/brain/aws298  1
2012 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. 13: 666. PMID 23176052 DOI: 10.1186/1471-2164-13-666  1
2012 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, et al. Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER. Journal of Neurovirology. 18: 511-20. PMID 23073667 DOI: 10.1007/s13365-012-0133-y  1
2012 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. Variation in germline mtDNA heteroplasmy is determined prenatally but modified during subsequent transmission. Nature Genetics. 44: 1282-5. PMID 23042113 DOI: 10.1038/ng.2427  1
2012 Hulgan T, Robbins GK, Kalams SA, Samuels DC, Grady B, Shafer R, Murdock DG, Selph D, Haas DW, Pollard RB, de Gruttola V, Snyder S, Nevin T, Pettinelli C, Dube M, et al. T cell activation markers and African mitochondrial DNA Haplogroups among non-hispanic black participants in AIDS clinical trials group study 384 Plos One. 7. PMID 22970105 DOI: 10.1371/journal.pone.0043803  1
2012 Damas J, Carneiro J, Gonçalves J, Stewart JB, Samuels DC, Amorim A, Pereira F. Mitochondrial DNA deletions are associated with non-B DNA conformations. Nucleic Acids Research. 40: 7606-21. PMID 22661583 DOI: 10.1093/nar/gks500  1
2012 Hudson G, Wilson I, Payne BI, Elson J, Samuels DC, Santibanez-Korev M, Hall SJ, Chinnery PF. Unique mitochondrial DNA in highly inbred feral cattle. Mitochondrion. 12: 438-40. PMID 22609322 DOI: 10.1016/j.mito.2012.05.003  1
2012 Pfeffer G, Blakely EL, Alston CL, Hassani A, Boggild M, Horvath R, Samuels DC, Taylor RW, Chinnery PF. Adult-onset spinocerebellar ataxia syndromes due to MTATP6 mutations. Journal of Neurology, Neurosurgery, and Psychiatry. 83: 883-6. PMID 22577227 DOI: 10.1136/jnnp-2012-302568  1
2012 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 Research and Human Retroviruses. 28: 759-65. PMID 22540188 DOI: 10.1089/AID.2011.0303  1
2012 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, et al. The use of next generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation. Mutation Research. 744: 154-60. PMID 22387842 DOI: 10.1016/j.mrgentox.2012.02.006  1
2012 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. 31: 112-29. PMID 22303991 DOI: 10.1080/15257770.2011.644101  1
2012 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. 12: 53. PMID 22299657 DOI: 10.1186/1471-2407-12-53  1
2012 Chinnery PF, Elliott HR, Hudson G, Samuels DC, Relton CL. Epigenetics, epidemiology and mitochondrial DNA diseases. International Journal of Epidemiology. 41: 177-87. PMID 22287136 DOI: 10.1093/ije/dyr232  1
2011 Song Z, Cao Y, Samuels DC. Replication pauses of the wild-type and mutant mitochondrial DNA polymerase gamma: a simulation study. Plos Computational Biology. 7: e1002287. PMID 22125488 DOI: 10.1371/journal.pcbi.1002287  1
2011 Gandhi VV, Samuels DC. Enzyme kinetics of the mitochondrial deoxyribonucleoside salvage pathway are not sufficient to support rapid mtDNA replication. Plos Computational Biology. 7: e1002078. PMID 21829339 DOI: 10.1371/journal.pcbi.1002078  1
2011 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 Journal of Acquired Immune Deficiency Syndromes. 58: 363-370. PMID 21792066 DOI: 10.1097/QAI.0b013e31822c688b  1
2011 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. 30: 317-39. PMID 21774628 DOI: 10.1080/15257770.2011.586955  1
2011 Payne BA, Wilson IJ, Hateley CA, Horvath R, Santibanez-Koref M, Samuels DC, Price DA, Chinnery PF. Mitochondrial aging is accelerated by anti-retroviral therapy through the clonal expansion of mtDNA mutations. Nature Genetics. 43: 806-10. PMID 21706004 DOI: 10.1038/ng.863  1
2011 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. Poor correlations in the levels of pathogenic mitochondrial DNA mutations in polar bodies versus oocytes and blastomeres in humans. American Journal of Human Genetics. 88: 494-8. PMID 21473984 DOI: 10.1016/j.ajhg.2011.03.010  1
2011 Pereira L, Soares P, Radivojac P, Li B, Samuels DC. Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity. American Journal of Human Genetics. 88: 433-9. PMID 21457906 DOI: 10.1016/j.ajhg.2011.03.006  1
2011 Stewart JD, Schoeler S, Sitarz KS, Horvath R, Hallmann K, Pyle A, Yu-Wai-Man P, Taylor RW, Samuels DC, Kunz WS, Chinnery PF. POLG mutations cause decreased mitochondrial DNA repopulation rates following induced depletion in human fibroblasts. Biochimica Et Biophysica Acta. 1812: 321-5. PMID 21138766 DOI: 10.1016/j.bbadis.2010.11.012  1
2011 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. Journal of Theoretical Biology. 271: 114-23. PMID 21130780 DOI: 10.1016/j.jtbi.2010.11.040  1
2011 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. Segregation of mtDNA throughout human embryofetal development: m.3243A>G as a model system. Human Mutation. 32: 116-25. PMID 21120938 DOI: 10.1002/humu.21417  1
2010 Samuels DC, Wonnapinij P, Cree LM, Chinnery PF. Reassessing evidence for a postnatal mitochondrial genetic bottleneck. Nature Genetics. 42: 471-2; author reply . PMID 20502486 DOI: 10.1038/ng0610-471  1
2010 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. Human Molecular Genetics. 19: 3043-52. PMID 20484224 DOI: 10.1093/hmg/ddq209  1
2010 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. American Journal of Human Genetics. 86: 540-50. PMID 20362273 DOI: 10.1016/j.ajhg.2010.02.023  1
2010 Song Z, Samuels DC. Analysis of enzyme kinetic data for mtDNA replication. Methods (San Diego, Calif.). 51: 385-91. PMID 20188839 DOI: 10.1016/j.ymeth.2010.02.019  1
2009 Samuels DC, Burn DJ, Chinnery PF. Detecting new neurodegenerative disease genes: does phenotype accuracy limit the horizon? Trends in Genetics : Tig. 25: 486-8. PMID 19819581 DOI: 10.1016/j.tig.2009.09.008  1
2009 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. American Journal of Human Genetics. 84: 628-40. PMID 19426953 DOI: 10.1016/j.ajhg.2009.04.013  1
2009 Cao Y, Samuels DC. Discrete stochastic simulation methods for chemically reacting systems. Methods in Enzymology. 454: 115-40. PMID 19216925 DOI: 10.1016/S0076-6879(08)03805-6  1
2009 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 Computational Biology. 5: e1000261. PMID 19132079 DOI: 10.1371/journal.pcbi.1000261  1
2008 Wonnapinij P, Chinnery PF, Samuels DC. The distribution of mitochondrial DNA heteroplasmy due to random genetic drift. American Journal of Human Genetics. 83: 582-93. PMID 18976726 DOI: 10.1016/j.ajhg.2008.10.007  1
2008 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. Molecular Biology and Evolution. 25: 2759-70. PMID 18845547 DOI: 10.1093/molbev/msn225  1
2008 Elliott HR, Samuels DC, Eden JA, Relton CL, Chinnery PF. Pathogenic mitochondrial DNA mutations are common in the general population. American Journal of Human Genetics. 83: 254-60. PMID 18674747 DOI: 10.1016/j.ajhg.2008.07.004  1
2008 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? Nature Genetics. 40: 275-9. PMID 18305478 DOI: 10.1038/ng.f.94  1
2008 Kang J, Samuels DC. The evidence that the DNC (SLC25A19) is not the mitochondrial deoxyribonucleotide carrier. Mitochondrion. 8: 103-8. PMID 18280798 DOI: 10.1016/j.mito.2008.01.001  1
2008 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. American Journal of Human Genetics. 82: 333-43. PMID 18252214 DOI: 10.1016/j.ajhg.2007.10.007  1
2008 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. Nature Genetics. 40: 249-54. PMID 18223651 DOI: 10.1038/ng.2007.63  1
2007 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. American Journal of Human Genetics. 81: 189-95. PMID 17564976 DOI: 10.1086/518901  1
2007 Samuels DC. Computational models of antiviral toxicity. Current Opinion in Drug Discovery & Development. 10: 43-8. PMID 17265740  1
2007 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. Journal of Medical Genetics. 44: 69-74. PMID 16950816 DOI: 10.1136/jmg.2006.043109  1
2006 Samuels DC. Mitochondrial AZT metabolism. Iubmb Life. 58: 403-8. PMID 16801215 DOI: 10.1080/15216540600791571  1
2006 Samuels DC, Carothers AD, Horton R, Chinnery PF. The power to detect disease associations with mitochondrial DNA haplogroups. American Journal of Human Genetics. 78: 713-20. PMID 16532401 DOI: 10.1086/502682  1
2005 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. 6: 136. PMID 16185363 DOI: 10.1186/1471-2164-6-136  1
2005 Bradshaw PC, Li J, Samuels DC. A computational model of mitochondrial AZT metabolism. The Biochemical Journal. 392: 363-73. PMID 16060859 DOI: 10.1042/BJ20050749  1
2005 Samuels DC. Life span is related to the free energy of mitochondrial DNA. Mechanisms of Ageing and Development. 126: 1123-9. PMID 15992863 DOI: 10.1016/j.mad.2005.05.003  1
2005 Bradshaw PC, Samuels DC. A computational model of mitochondrial deoxynucleotide metabolism and DNA replication. American Journal of Physiology. Cell Physiology. 288: C989-1002. PMID 15634740 DOI: 10.1152/ajpcell.00530.2004  1
2004 Samuels DC, Schon EA, Chinnery PF. Two direct repeats cause most human mtDNA deletions. Trends in Genetics : Tig. 20: 393-8. PMID 15313545 DOI: 10.1016/j.tig.2004.07.003  1
2004 Samuels DC. Mitochondrial DNA repeats constrain the life span of mammals. Trends in Genetics : Tig. 20: 226-9. PMID 15109774 DOI: 10.1016/j.tig.2004.03.003  1
2003 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. The Journal of Clinical Investigation. 112: 1351-60. PMID 14597761 DOI: 10.1172/JCI19435  1
2003 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 Research. 31: 6043-52. PMID 14530452  1
2003 Capps GJ, Samuels DC, Chinnery PF. A model of the nuclear control of mitochondrial DNA replication. Journal of Theoretical Biology. 221: 565-83. PMID 12713941  1
2002 Barenghi CF, Hulton S, Samuels DC. Polarization of superfluid turbulence. Physical Review Letters. 89: 275301. PMID 12513214 DOI: 10.1103/PhysRevLett.89.275301  1
2002 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 (London, England). 360: 1323-5. PMID 12414225 DOI: 10.1016/S0140-6736(02)11310-9  1
2002 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. Neuromuscular Disorders : Nmd. 12: 858-64. PMID 12398838 DOI: 10.1016/S0960-8966(02)00047-0  1
2002 Barenghi CF, Samuels DC. Evaporation of a packet of quantized vorticity. Physical Review Letters. 89: 155302. PMID 12365997 DOI: 10.1103/PhysRevLett.89.155302  1
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