David Samuels’ peer-reviewed publications in chronological order

Links to full text are in the paper names

2019

Mitochondrial DNA Haplogroups and Delirium During Sepsis

Samuels, David C.; Hulgan, Todd ; Fessel, Joshua P. ; Billings, Frederic T. ; Thompson, Jennifer L. ; Chandrasekhar, Rameela ; Girard, Timothy D. Critical Care Medicine, 47 (8) 1065-1071.

 

Genomic and transcriptomic characterization of the mitochondrial-rich oncocytic phenotype on a thyroid carcinoma background

Cavadas, Bruno; Pereira, Joana B. ; Correia, Marcelo ; Fernandes, Veronica ; Eloy, Catarina ; Sobrinho-Simoes, Manuel ; Soares, Paula ; Samuels, David C. ; Maximo, Valdemar; Pereira, Luisa, Mitochondrion, 46 pg 123-133.

Nuclear-Mitochondrial interactions influence susceptibility to HIV-associated for neurocognitive impairment

Smieszek, S.; Jia, P. ; Samuels, D. C. ; Zhao, Z.; Barnholtz-Sloan, J. ; Kaur, H. ; Letendre, S.; Ellis, R.; Franklin, D. R. ; Hulgan, T.; Kallianpur, A. ; Bush, W. S., Mitochondrion, 46 pg 247-255.

Cerebrospinal Fluid Ceruloplasmin, Haptoglobin, and Vascular Endothelial Growth Factor Are Associated with Neurocognitive Impairment in Adults with HIV Infection

Kallianpur, A. R. ; Gittleman, H.; Letendre, S. ; Ellis, R.; Barnholtz-Sloan, J. S. ; Bush, W. S.; Heaton, R. ; Samuels, D. C. ; Franklin, D. R., Jr. ; Rosario-Cookson, D.; Clifford, D. B. ; Collier, A. C. ; Gelman, B.; Marra, C. M. ; McArthur, J. C.; McCutchan, J. A. ; Morgello, S. ; Grant, I. ; Simpson, D.; Connor, J. R. ; Hulgan, T. ; McArthur, Justin ; Morgello, Susan ; Simpson, David ; McCutchan, J. Allen ; Collier, Ann ; Marra, Christina; Clifford, David ; Gelman, Benjamin, Molecular Neurobiology, 56(5) 3808-3818.

Identification of serum metabolites associating with chronic kidney disease progression and anti-fibrotic effect of 5-methoxytryptophan

Chen, Dan-Qian ; Cao, Gang; Chen, Hua ; Argyopoulos, Christos P. ; Yu, Hui ; Su, Wei ; Chen, Lin ; Samuels, David C. ; Zhuang, Shougang; Bayliss, George P. ; Zhao, Shilin ; Yu, Xiao-Yong; Vaziri, Nosratola D. ; Wang, Ming ; Liu, Dan; Mao, Jia-Rong ; Ma, Shi-Xing; Zhao, Jin ; Zhang, Yuan ; Shan, You-Quan ; Kang, Huining); Ye, Fei; Cheng, Xiao-Hong ; Li, Xiang-Ri; Zhang, Li ; Meng, Mei-Xia ; Guo, Yan ; Zhao, Ying-Yong, Nature Communications, 10 art 1476.

Genomic Positional Dissection of RNA Editomes in Tumor and Normal Samples

Chigaev, Michael ; Yu, Hui ; Samuels, David C. ; Sheng, Quanhu; Oyebamiji, Olufunmilola ; Ness, Scott; Yue, Wei; Zhao, Ying-Yong ; Guo, Yan, Frontiers in Genetics, 10 art 211.

Architectures and accuracy of artificial neural network for disease classification from omics data

Yu, Hui ; Samuels, David C. ; Zhao, Ying-yong; Guo, Yan, BMC Genomics, 20 art 167.

Single-nucleotide variants in human RNA: RNA editing and beyond

Guo, Yan; Yu, Hui; Samuels, David C.; Yue, Wei ; Ness, Scott; Zhao, Ying-yong, Briefings in Functional Genomics, 18(1) 30-39

 

 

2018

Quality and concordance of genotyping array data of 12,064 samples from 5840 cancer patients

Mingsheng Guo, Wei Yue, David C. Samuels, Hui Yu, Jing He, Ying-Yong Zhao, Yan Guo, Genomics. 111(4) 950-957

 

Tri-allelic heteroplasmies, DNA-RNA differences and their polynucleotide tract associations in the mitochondrial genome

Shilin Zhao, David C. Samuels, Ying-Yong Zhao, Yan Gou,Genomics, 110(4) 211-220

 

Mutation-specific effects in germline transmission of pathogenic mtDNA variants

Auke B.C. Otten, Suzanne C.E.H. Sallevelt, Phillippa J. Carling, Joseph C.F.M. Dreesen, Marion Drusedau, Sabine Spierts, Aimee D.C. Paulussen, Christine E.M. de Die-Smulders, Mary Herbert, Patrick F. Chinnery, David C. Samuels, Patrick Lindsey, Hubert J.M. Smeets,  Human Reproduction 33(7) 1331-1341

 

Relation of body mass index to symptom burden in patients with atrial fibrillation

Brandon Chalazan, Deanna Disckerman, Arvind Sridhar, Maureen Farrell, Katherine Gayle, David C. Samuels, Benjamin Shoemaker, Dawood Darbar, American Journal of Cardiology 122(2) 235-241

 

Hemochromatosis (HFE) gene variants are associated with increased mitochondrial DNA levels during HIV-1 infection and antiretroviral therapy

Asha R. Kallianpur, Mariana Gerschenson, Todd Hulgan, Harpreet Kaur, David B. Clifford, David W. Haas, Deborah G. Murdock, Justin C. McArthur, David C. Samuels, David M. Simpson, AIDS Research and Human Retroviruses, 34(11) 942-949

 

The role of mitochondrial DNA variation in age-related decline in gait speed among older men living with human immunodeficiency virus

Jing Sun, Todd T. Brown, David C. Samuels, Todd Hulgan, Gypsyamber D’Souza, Beth D. Jamieson, Kristine M. Erlandson, Jeremy Martinson, Frank J. Palella, Joseph B. Margolick, Gregory D. Kirk, Jennifer Schrack, Clinical Infectious Diseases 67(5) 778-784

 

Cereberospinal fluid Ceruloplasmin, Haptoglobin and vascular endothelial growth factor are associated with neurocognitive impairment in adults with HIV infection

Asha R. Kallianpur, Hayley Gittleman, Scott Letendre, Ronald Ellis, Jill S. Barnholtz-Sloan, William S. Bush, Ronald Heaton, David C. Samuels, Donald R. Franklin, Debralee Rosario-Cookson, David B. Clifford, Benjamin B. Gelman, Christina M. Marra, Justin C. McArthur, J. Allen McCutchan, Susan Morgello, Igor Grant, David M. Simpson, James R. Connor, Todd Hulgan, Molecular Neurobiology 56(5) 3808-3818

 

Strategies for processing and quality control of Illumina genotyping arrays

Shilin Zhao, Wang Jing, David C. Samuels, Quanghu Sheng, Yu Shyr, Yan Guo,  Briefings in Bioinformatics 19(5) 765-775

 

Single-nucleotide variants in human RNA: RNA editing and beyond

Yan Guo, Hui Yu, David C. Samuels, Wei Yue, Scott Ness, Ying-Yong Zhao, Briefings in Functional Genomics 18(1) 30-39

 

Peripheral blood mitochondrial DNA copy number obtained from genome-wide genotype data is associated with neurocognitive impairment in persons with chronic HIV infection

Todd Hulgan, Asha Kallianpur, Yan Guo, Jill Barnholtz-Sloan, Haley Gittleman, Todd Brown, Ronald Ellis, Scott Letendre, Robert Heaton, David C. Samuels (2018), JAIDS.80(4) 95-102

 

Bi-stream CNN Down Syndrome screening model based on genotyping array

Bing Feng, William Hoskins, Yan Zhang, Zibo Meng, David C. Samuels, Yan Guo, Jijun Tang, BMC Medical Genomics 11(5) art 105

 

Power and sample size calculations for high-throughput sequencing-based experiments

Chung-I Li, David C. Samuels, Ying-Yong Zhao, Yu Shyr, Yan Guo, Briefings in Bioinformatics 19(6) 1247-1255

 

2017

The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data

Yan Guo, Shilin Zhao, Quanhu Sheng, David C. Samuels, Yu Shy,  BMC Genomics, 18(6) article 690

 

StrandScript: evaluation of Illumina genotyping array design and strand correction

Jing Wang, David C. Samuels, Yu Shyr, Yan Guo,  Bioinformatics, 33(15) 2399-2401

 

Multi-perspective quality control of Illumina sequencing data analysis

Quanhu Sheng, Kasey Vickers, Shilin Zhao, Jing Wang, David C. Samuels, Olivia Koues, Yu Shyr, Yan Gu,  Briefings in Functional Genomics, 16 (4) 194-204

 

Genome-wide association study of HIV-associated neurocognitive disorder (HAND): A CHARTER group study

Peilin Jia, Zhongming Zhao, Todd Hulgan, William S. Bush, David C. Samuels, Cinnamon S. Bloss, Robert K. Heaton, Ronald J. Ellis, Nicholas Schork, Christina M. Marra, Ann C. Collier, David B. Clifford, Benjamin B. Gelman, Ned Sacktor, Susan Margello, David M. Simpson, J. Allen McCutchan, Jill S. Barnholtz-Sloan, Donald R. Franklin, Debralee Rosario, Scott L. Letendre, Igor Grant, Asha R. Kallianpur, American Journal of Medical Genetics part B – Neuropsychiatric Genetics, 174(4) 413-426

 

Cerebrospinal fluid (CSF) biomarkers of iron status are associated with CSF viral load, antiretroviral therapy, and demographic factors in HIV-infected adults

Stephanie M. Patton, Quan Wang, Todd Hulgan, James R. Connor, Peilin Jia, Zhongming Zhao, Scott L. Letendre, Ronald J. Ellis, William S. Bush, David C. Samuels, Donald R. Franklin, Harpreet Kaur, Jennifer Iudicello, Igor Grant, Asha R. Kallianpur,  Fluids and Barriers of the CNS, 14 article 11

 

Improvements and impacts of GRCh38 human reference on high throughput sequencing data analysis

Yan Guo, Yulin Dai, Huo Yu, Shilin Zhao, David C. Samuels, Yu Shyr,  Genomics, 109(2) 83-90

 

OSBPL10m RXRA and lipid metabolism confer African-ancestry protection against dengue haemorrhagic fever in admixed Cubans

Beatriz Sierra, Petr Triska, Pedro Soares, Gissel Garcia, Ana B. Perez, Eglys Aguirre, Marisa Oliveira, Bruno Cavadas, Be A. Atrice Regnault, Mayling Alverez, Didye Ruiz, David C. Samuels, Anavaj Sakuntabhai, Luisa Pereira, Maria G. Guzman, PLoS Pathagens, 13(2) article e1006220

 

Mitochondrial haplogroups affect severity but not prevalence of diabetic retinopathy

Jana A. Bregman, David J. Herren, Christopher B. Estopinal, Isaac M. Chocron, Paula A. Harlow, Cassandra Warden, Milam A. Brantley Jr.,  David C. Samuels (2017), Investigative Ophthalmology & Visual Science, 58(2) 1346 – 1351

 

Estimating relative mitochondrial DNA copy number using high throughput sequencing data

Pan Zhang, Brian D. Lehmann, David C. Samuels, Shilin Zhao, Ying-Yong Zhao, Yu Shyr, Yan Guo, Genomics 109(5-6) 457-462

 

Current research on non-coding ribonucleic acid (RNA)

Jing Wang, David C. Samuels, Shilin Zhao, Yu Xiang, Yan Guo, Genes, 8(12) Article 366 (20 pages)

 

Mitochondrial haplogroups modify the effect of diabetes duration and HbA1c on proliferative diabetic retinopathy risk in patients with type 2 diabetes

Sabrina L. Mitchell, Abigail C. Neininger, Carleigh N. Bruce, Isaac M. Chocron, Jana Bregman, Christopher B. Estopinal, Ayesha Muhammad, Allison C. Umfress, Kelli L. Jarell, Cassandra Warden, Paula Harlow, Melissa Wellons, David C Samuels, Milam A, Brantley, Investigative Ophthalmology & Visual Science 58(14) 6481-6488

 

Strategies for equitable pharmacogenomics-guided Warfarin dosing among European and African American individuals in a clinical population

Laura K. Wiley, Jacob P. VanHouten, David C. Samuels, Melinda C. Aldrich, Dan M. Roden, Josh F. Peterson, Joshua C. Denny,  Pacific Symposium on Biocomputing Proceedings 22, pages 545-556

 

2016

Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck

Ian J Wilson, Phillipa J. Carling, Charlotte L. Alston, Vasileios I. Floros, Angela Pyle, Gavin Hudson, Suzanne C.E.H. Sallevelt, Costana Lamperti, Valeria Carelli, Laurence A. Bindoff, David C. Samuels, Passorn Wonnapinij, Massimo Zeviani, Robert W. Taylor, Hubert J.M. Smeets, Rita Horvath, Patrick F. Chinnery, Human Molecular Genetics 25(5) 1031-1041

 

Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequence data

Pan Zhang, David C. Samuels, Brian Lehmann, Thomas Stricker, Jennifer Pientenpol, Yu Shyr, Yan Guo,  Briefings in Bioinformatics 17(2), 224-232

 

Mitochondria single nucleotide variation across six blood cell types

Pan Zhang, David C. Samuels, Jing Wang, Shilin Zhao, Yu Shyr, Yan Guo, Mitochondrion 28, 16-22

 

European mitochondrial DNA haplogroups are associated with cerebrospinal fluid biomarkers of inflammation in HIV infection

David C. Samuels, Asha R. Kallianpur, Ronald J. Ellis, William S. Bush, Scott Letendre, Donald Franklin, Igor Grant, Todd Hulgan, Pathogens & Immunity 1(2) 330-351

 

Homeostatic responses regulate selfish mitochondrial genome dynamics in C. elegans

Bryan L. Gitschlag, Cait S. Kirby, David C. Samuels, Rama D. Gangula, Simon A. Mallal, Maulik R. Patel,  Cell Metabolism 24(1), 91-103

 

Mitochondrial haplogroups as a risk factor for herpes zoster

Rebecca T. Levinson, Todd Hulgan, Spyros A Kalams, Joshua P Fessel, David C. Samuels, Open Forum Infectious Diseases. 3(4) 

 

Practicability of mitochondrial heteroplasmy detection through an Illumina genotyping array

Pan Zhang, David C. Samuels, Shilin Zhao, Jing Wang, Yu Shyr, Yan Guo, Mitochondrion, 75-78

 

Heterozygosity ratio, a robust global genomic measure of autozygosity and its association with height and disease risk

David C. Samuels, Jing Wang, Fei Ye, Jing He, Rebecca T. Levinson, Quamhu Sheng, Shilin Zhao, John A. Capra, Yu Shyr, Wei Zheng, Yan Guo, Genetics 204(3) 893-904

 

2015

RNAseq by total RNA library identifies additional RNAs compared to poly(A) RNA library

Yan Guo, Shilin Zhao, Quanhu Sheng, Mingsheng Guo, Brian Lehmann, Jennifer Pietenpol, David C. Samuels, Yu Shyr, Biomed Research International Article ID 862130

 

Genome measures used for quality control are dependent on gene function and ancestry

Jing Wang, Leon Raskin, David C. Samuels Yu Shyr, Yan Guo (2015) Bioinformatics  31(3) 318-323

 

Alternative applications for distinct RNA sequencing strategies

Leng Han, Kasey C. Vickers, David C. Samuels, Yan Guo (2015) Briefings in Bioinformatics 16(4) 629-639

 

Fine time scaling of purifying selection on human nonsynonymous mtDNA mutations based on the worldwide population tree and mother-child pairs. 

Bruno Cavadas, Pedro Soares, Rui Camacho, Andreia Brandao, Marta D. Costa, Veronica Fernandes, Joana B. Pereira, Teresa Rito, David C. Samuels, Luisa Pereira Human Mutation 36(11) 1100-1111

 

Mitochondrial DNA haplogroups and neurocognitive impairment during HIV infection

Todd Hulgan, David C. Samuels, William Bush, Ronald J. Ellis, Scott L. Letendre, Robert K. Heaton, Donald R. Franklin, Peter Straub, Deborah G. Murdock, David B. Clifford, Ann C. Collier, Benjamin B. Gelmon, Christina M. Marra, Justin C. McArthur, J. Allen McCutchan, Susan, Morgello, David M. Simpson, Igor Grant & Asha R. Kallianpur for the CHARTER Group, Clinical Infectious Diseases 61(9) 1476-1484

 

2014

Illumina human exome genotyping array clustering and quality control

Yan Guo, Jing He, Shilin Zhao, Hui Wu, Xue Zhong, Quanhu Sheng, David C. Samuels, Yu Shyr, Jirong Long (2014), Nature Protocols, 9(11) 2643-2662.

 

Mitochondrial haplogroups are associated with severity of diabetic retinopathy

Christopher B. Estopinal, Isaac M. Chocron, Megan B. Parks, Emily A. Wade, Rachel M. Roberson, L. Goodwin Burgess, Milam A. Brantley Jr, David C. Samuels (2014) Investigative Ophthalmology & Visual Science 55(9) 5589-5595

 

 

Genetic Variation in iron metabolism is associated with neuropathic pain and pain severity in HIV-infected patients on antiretroviral therapy

Asha R. Kallianpur, Peilin Jia, Ronald J. Ellis, Zhongming Zhao, Cinnamon Bloss, Wanqing Wen, Christina M. Marra, Todd Hulgan, David M. Simpson, Susan Morgollo, Justin C. McArthur, David B. Clifford, Ann C. Collier, Benjamin B. Gelman, J. Allen, McCutchan, Donald Franklin, David C. Samuels, Debralee Rosario, Emily Holzinger, Deborah G. Murdock, Scott Letendre, Igor Grant for the CHARTER Study Group, (2014) PLoS One, 9(8) e103123

 

High-throughput sequencing in mitochondrial DNA research

Fei Ye, David C. Samuels, Travis Clark, Yan Guo (2014) Mitochondrion 17, 157-163

 

Data from artificial models of mitochondrial DNA disorders are not always applicable to humans

Julie Steffan, Nadine Gigarel, David C. Samuels, Sophie Monnot, Roxana Borghese, Laetitia Hesters, Nelly Frydman, Philippe Burlet, Rene Frydman, Alexandra Benachi, Agnes Rotig, Arnold Munnich, Jean-Paul Bonnefont (2014) Cell Reports 7(4) 933-934

 

 

Global human frequencies of predicted nuclear pathogenic variants and the role played by protein hydrophobicity in pathogenicity potential

Luisa Periera, Pedro Soares, Petr Triska, Teresa Rito, Agnes van der Waerden, Biao Li, Predrag Radivojac, David C Samuels (2014), Scientific Reports. 4:7155

 

Epidermal nerve fiber density, oxidative stress and mitochondrial haplogroups in HIV-infected Thais initiating therapy

T. Hulgan, R.T. Levinson, M. Gerschenson, N. Phanuphak, J. Ananworanich, N. Teeratakulpisarm, T. Jadwattanakul, D.E. LiButti, H. Fink, J.C. McArthur, G.J. Ebenezer, P.Hauer, D. Murdock, C.M. Shikuma, D.C. Samuels,. AIDS 28(11) 1625-1633.

 

High Proportion of Heteroresistance in gyrA and gyrB in fluoroquinolone resistant Mycobacterium tuberculosis clinical isolates

Brandon Eilertson, Fernanda Maruri, Amondrea Blackman, Miguel Herrera, David C. Samuels, Timothy R. Sterling, Antimicrobial Agents and Chemotherapy 58(6) 3270-3275

 

Mitochondrial DNA rearrangements in health and disease — A comprehensive study

Joana Damas, David C. Samuels, Joao Carneiro, Antonio Amorim, Filipe Pereira (2014), Human Mutation 35(1) 1-14.

 

Multi-perspective quality control of Illumina exome sequencing data using QC3

Yan Guo, Shilin Zhao, Quanhu Sheng, Fei Ye, Jiang Li, Brian Lehmann, Jennifer Pientenpol, David C. Samuels, Yu Shyr (2014) Genomics 103(5-6) 323-328.

 

2013

The Other Genome: A Systematic Review of Studies of Mitochondrial DNA Haplogroups and Outcomes of HIV Infection and Antiretroviral Therapy.

Hart AB, Samuels DC, Hulgan T (2013) AIDS Rev. 2013 Oct-Dec;15(4):213-20 PMID: 24322381

 

Recurrent tissue-specific mtDNA mutations are common in humans

David C. Samuels, Chun Li, Bingshan Li, Zhuo Song, Eric Torstenson, Hayley Boyd Clay, Antonis Rokas, Tricia A Thortnon-Wells, Jason H. Moore, Tia M. Hughes, Robert D. Hoffman, Jonathan L. Haines, Deborah G. Murdock, Douglas P. Mortlock, Scott M. Williams (2013) PLoS Genetics 9(11) e1003929 PMC3820769.

 

Comparative Study of Exome Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as Control

Yan Guo, Quagho Sheng, David C. Samuels, Brian Lehmann, Joshua Bauer, J.A. Pietenpol, Yu Shyr (2013), BioMed Research International.

 

Three stage quality control strategies for DNA re-sequencing data

Yan Guo, Sheng Quanghu, Fei Ye, Travis Clark, David C. Samuels (2013), Briefings in Bioinformatics. 15(6) 879-889

 

 

Finding the Lost Treasures in Exome Sequencing Data

David C. Samuels, Leng Han, Jiang Li, Sheng Quanhu, Travis A. Clark, Yu Shyr, Yan Gou (2013), Trends in Genetics. 29(10) 593-599

 

 

Large scale comparisons of gene expression levels by microarrays and RNAseq using TCGA data

Yan Guo, Quanhu Sheng, Jiang Li, Fei Ye, David C. Samuels, Yu Shyr (2013) PLoS One. 8(8) e71462

 

MitoSeek: Extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

Yan Guo, Jiang Li, Chung-I Li, Yu Shyr, David C Samuels (2013) Bioinformatics, 29 (9) 1210-1211.

 

Mutation dependence of the mitochondrial DNA copy number in the first stages of human embryogenesis

Sophie Monnot, David C. Samuels, Laetitia Hesters, Nelly Frydman, Nadine Gigeral, Philippe Burlet, Violaine Kerbrat, Frederic Lamazou, Rene Frydman, Alexandra Benachi, Josue Feingold, Agnes Rotig, Arnold Munnich, Jean-Paul Bonnefont and Julie Steffann (2013), Human Molecular Genetics, 22 (9) 1867-1872.

 

Evaluating Purifying Selection in the Mitochondrial DNA of Various Mammalian Species

Pedro Soares, Diogo Abrantes, Teresa Rito, Noel Thomson, Predrag Radivojac, Biao Li, Vincent Macauley, David C. Samuels, Luisa Pereira (2013), PLoS One, 8 (3), e58993 PMC3606437

 

Mitochondrial genomics and antiretroviral therapy-associated metabolic complications in HIV-infected black South Africans: a pilot study

Phumla Z. Sinxadi, Joel A. Dave, David C. Samuels, Jeannine M. Heckmann, Gary Maartens, Naoimi S. Levitt, C. William Wester, David W. Haas, Todd Hulgan (2013) AIDS research and Human Retroviruses. 29 (7) 1031-1039 PMID 23428049

 

 

Preventing the transmission of pathogenic mitochondrial DNA mutations: can we achieve long-term benefits from germ-line gene transfer?

David C. Samuels, Passorn Wonnapinij, Patrick F. Chinnery (2013) Human Reproduction 28(3), 554-559. PMC3571501

 

 

Evaluation of Allele Freqency Estimation Using Pooled Sequencing Data Simulation

Yan Guo, David C. Samuels, Jiang Li, Travis Clark, Chung-I Li, Yu Shyr (2013), The Scientific World Journal article ID 895496 (9 pages). PMC3582166

 

Universal heteroplasmy of human mitochondrial DNA

Brendan A. I. Payne, Ian J. Wilson, Patrick Yu-Wai-Man, Jon Coxhead, David Deehan, Rita Horvath, Robert W. Taylor, David C. Samuels, Mauro Santibanez-Koref, and Patrick F. Chinnery. (2013) Human Molecular Genetics 22(2) 384-390. PMC3526165

 

No evidence of an association between mitochondrial DNA variants and osteoarthritis in 7410 cases and 5200 controls

Gavin Hudson, Kalliope Panoutsopoulou, Ian Wilson, Lorraine Southam, Nigel W. Rayner, Nigel Arden, Fraser Birrell, Ian Carluke, Andrew Carr, Kay Chapman, Panos Deloukas, Michael Doherty, Andrew McCaskie, William E.R. Ollier, Stuart H. Ralston, Mike R. Reed, Tim D. Spector, Ana M. Valdes, Gillian A. Wallis, J. Mark Wilkinson, Eleftheria Zeggini, arcOGEN Consortium, David C Samuels, John Loughlin, Patrick F. Chinnery (2013), Annals of the Rheumatic Diseases (72) 136-139. PMC3551219

 

 

2012

Non-random mtDNA segregation patterns indicate a metastable heteroplasmic segregation unit in m.3243A>G cybrid cells

Anton K. Raap, Roshan S. Jahangor Tafrechi, Frans M. van de Rijke, Angela Pule, Carolina Wahlby, Karoly Szuhai, Raimond B.G. Ravelli, Rene F.M. de Coo, Harsha K. Rajasinha, Mats Nilsson, Patrick F. Chinnery, David C. Samuels and George M.C. Janssen (2012), PLoS One 7(12) e52080 PMC3525564

 

The effect of strand bias in Illumina short-read sequencing data

Yan Guo, Jiang Li, Chung-I Li, Jirong Long, David C. Samuels, Yu Shyr (2012), BMC Genomics 13:666. PMC3532123

 

Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER

Emily R. Holzinger, Todd Hulgan, Ronald J. Ellis, David C. Samuels, Marylyn D. Ritchie, David W. Haas, Asha R. Kallianpur, Cinnamon S. Bloss, David B. Clifford, Ann C. Collier, Benjamin B. Gelman, Christina M. Marra, Justin C. McArthur, J. Allen McCutchan, Susan Morgello, David M. Simpson, Donald R. Franklin, Debralee Rosario, Doug Selph, Scott Letendre, and Igor Grant for the CHARTER Group (2012) Journal of NeuroVirology (18) 511-520 PMC3587171

 

 

Variation in germline mtDNA heteroplasmy is determined prenatally but modified during subsequent transmission

Christoph Freyer, Lynsey M Cree, Arnoud Mourier, James B Stewart, Camilla Koolmeister, Dusanka Milenkovac, David C Samuels, Nils-Goran Larsson, Patrick F Chinnery (2012), Nature Genetics (44) 1282-1285. PMC3492742

 

 

What is influencing the phenotype of the common homozygous polymerase gamma mutation p.Ala467Thr?

Vivienne C.M. Neeve, David C. Samuels Laurence Bindoff, Bianca van den Bosch, Gert Van Goethem, Bert Smeets, Anne Lombes, Michio Hirano, Salvatore DiMauro, Maaike De Vries, Jan Smeitink, Bart Smits, Carsten Saft, Bianca-Cortina Keiling, Birgit Czermin, Angela Abicht, Hanns Lochmüller, Gavin Hudson, Grainne G. Gorman, Doug M. Turnbull, Robert W. Taylor, Elke Holinski-Feder, Patrick F. Chinnery, Rita Horvath (2012) Brain (135) 3614-3626. PMC3525059

 

 

T cell Activation Markers and African Mitochondrial DNA Haplogroups among Non-Hispanic Black Participants in AIDS Clinical Trials Group Study 384

Todd Hulgan, Gregory K. Robbins, Spyros A. Kalams, David C. Samuels, Benjamin Grady, Robert Shafer, Deborah G. Murdock, Doug Selph, David W. Haas, and Richard B. Pollard for the AIDS Clinical Trials Group. (2012) PLoS One 7(8) article e43803. PMC3433792

 

 

Unique mitochondrial DNA in highly inbred feral cattle

G. Hudson, I. Wilson, B.I.A. Payne, J. Elson, D.C. Samuels, M.Santibanez-Korev, S.J.G. Hall, P.F. Chinnery (2012), Mitochondrion 12, 438-440.

 

Risk Factors for Symptomatic Hyperlactatemia and Lactic Acidosis Among Combination Antiretroviral Therapy-Treated Adults in Botswana: Results From a Clinical Trial

C.W. Wester, S.K. Eden, B.E. Shepherd, H. Bussman, V. Novitsky, D.C. Samuels, S.L. Hendrickson, C.A. Winkler, S.J. O’Brien, M. Essex, R.T. D’Aquila, V. deGruttola, R. G. Marlink (2012) AIDS Research and Human Retroviruses 28, 759-765.

 

 

Adult onset spinocerebellar ataxia syndromes due to MTATP6 mutations

G. Pfeffer, A. Hassani, E.L. Blakely, C.L. Alston, M. Boggild, R. Horvath, D.C. Samuels, R.W. Taylor, P.F. Chinnery (2012), Journal of Neurology, Neurosurgery and Psychiatry 83, 883-886.

 

 

The use of next-generation sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation

Y. Guo, Q. Cai, D.C. Samuels, F. Ye, J. Long, C.-I. Li, J.F. Winther, E.J. Tawn, M. Stovall, P. Lahteenmaki, N. Malia, S. Levy, C. Shaffer, Y. Shyr, X. Shu, J.D. Boice Jr (2012) Mutation Research – Genetic Toxicology and Environmental Mutagenesis 744, 154-160. PMC3354959

 

 

Mitochondrial DNA deletions are associated with non-B DNA conformations

J. Damas, J. Carneiro, J. Goncalves, J.B.  Stewart, D.C. Samuels, A. Amorim, F. Pereira (2012), Nucleic Acids Research 40(16) 7606-7621. PMC3439893

 

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

L. Periera, P. Soares, V. Maximo, D.C. Samuels (2012), BMC Cancer 12:53 (10 pages). PMC3342922

 

Correlated Tissue Expression of Genes of Cytoplasmic and Mitochondrial Nucleotide Metabolisms in Normal Tissues is Disrupted in Transformed Tissues

V.V. Gandhi, D.C. Samuels (2012), Nucleosides, Nucleotides and Nucleic Acids 31, 112-129. PMC3464496

 

Epigenetics, epidemiology and mitochondrial DNA diseases

P.F. Chinnery, H.R. Elliot, G. Hudson, D.C. Samuels, C.L. Relton (2012), International Journal of Epidemiology 41, 177-187.

 

 

2011

Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study

Z. Song, Y. Cao, D.C. Samuels (2011), PLoS Computational Biology 7(11), e1002287.

 

Mitochondrial Genomics and CD4 T-cell count recovery after antiretroviral therapy initiation in AIDS clinical trials group study 384

B.J. Grady, D.C. Samuels, G.K. Robbins, D. Selph, J.A. Canter, R.B. Pollard, D.W. Haas, R. Shafer, S.A. Kalams, D.G. Murdock, M.D. Ritchie, T.  Hulgan (2011), Journal of AIDS 58(4), 363-370. PMC3204178

 

Enzyme kinetics of the mitochondrial deoxyribonucleoside salvage pathway are not sufficient to support rapid mtDNA replication

V.V. Gandhi, D.C. Samuels (2011), PLoS Computational Biology 7(8), e1002078. PMC3150320

 

A review comparing deoxyribonucleoside triphosphate (dNTP) concentrations in the mitochondrial and cytoplasmic compartments of normal and transformed cells

V.V. Gandhi, D.C. Samuels (2011) Nucleosides, Nucleotides and Nucleic Acids 30(5), 317-339. PMC3210641

 

Mitochondrial aging is accelerated by anti-retroviral therapy through clonal expansion of mtDNA mutations

B.A.I. Payne, I.J. Wilson. C.A. Hateley, R. Horvath, M. Santibanez-Koref, D.C. Samuels, D.A. Price, P.F. Chinnery (2011), Nature Genetics 43 (8), 806-810. PMC3223397

 

 

Comparing phylogeny and the predicted pathogenicity of protein variations reveals equal purifying selection across the global human mtDNA diversity

L. Pereira, P. Soares, P. Radivojac, B. Li, D.C. Samuels (2011), American Journal of Human Genetics 88, 433-439. PMC3071914

 

 

Poor Correlations in the levels of pathogenic mitochondrial DNA mutations in polar bodies versus oocytes and blastomeres in humans

N. Gigarel, L. Hester, D.C. Samuels, S. Monnot, P. Burlet, V. Kerbrat, F. Lamazou, A. Benachi, R. Frydman, J. Feingold, A. Rotig, A. Munnich, J.P. Bonnefont, N. Frydman, J. Steffann (2011) American Journal of Human Genetics 88, 494-498.

 

 

Segregation of mtDNA throughout human embryofetal development: m3243A>G as a model system

S. Monnot, N. Gigarel, D.C. Samuels, P. Burlet, L. Hesters, N. Frydman, R. Frydman, V. Kerbrat, B. Funalot, J. Martinovic, A. Benachi, J. Feingold, A. Munnich, J-P. Bonnefont, J. Steffann. (2011) Human Mutation 32(1), 116-125. PMC3058134.

 

POLG mutations cause decreased mitochondrial DNA repopulation rates following induced depletion in human fibroblasts

J.D. Stewart, S, Schoeler, K.S. Sitarz, R. Horvath, K. Hallmann, A. Pyle, P. Yu-Wai-Man, R.W. Taylor, D.C. Samuels, W.S. Kunz, P.F. Chinnery (2011), Biochemica et Biophysica Acta 1812, 321-325. PMID:21138766.

 

The BCL-2-associated death promoter (BAD) lowers the threshold at which the BCL-2-interacting domain death agonist (BID) triggers mitochondria disintegration

C.C. Howells, W.T. Baumann, D.C. Samuels, C.V. Finkielstein (2011), Journal of Theoretical Biology 271, 114-123. PMID:21130780.

 

2010

OPA1 mutations cause cytochrome c oxidase deficiency due to loss of wild-type mtDNA molecules

P. Yu-Wai-Man, K.S. Sitarz, D.C. Samuels, P.G. Griffiths, A.K. Reeve, L.A. Bindoff, R. Horvath, P.F. Chinnery (2010), Human Molecular Genetics 19(15), 3043-3052. PMC2901142.

 

 

Reassessing evidence for a postnatal mitochondrial genetic bottleneck

D.C. Samuels, P. Wonnapinij, L.M. Cree, P.F. Chinnery, (2010), Nature Genetics 42(6), 471-472. PMID:20502486.

 

Analysis of enzyme kinetic data for mtDNA replication

Z. Song, D.C. Samuels, (2010), Methods 51(4), 385-391. PMC2903644

 

 

Information for genetic management of mtDNA disease: Sampling pathogenic mtDNA mutants in the human germline and in placenta

D.R. Marchington, S. Malik, A. Banerjee, K, Turner, D. Samuels, V. Macauley, P Oakeshott, C. Fratter, S.H. Kennedy, J. Poulton (2010) Journal of Medical Genetics, 47, 257-261.

 

 

Previous estimates of mitochondrial DNA mutation level variance did not account for sampling error: Comparing the mtDNA genetic bottleneck in mice and humans

P. Wonnapinij, P.F. Chinnery, D.C. Samuels (2010), American Journal of Human Genetics 86(4) 540-550. PMC2850432.

 

 

2009
The diversity present in 5140 human mitochondrial genomes

L. Pereira, F. Freitas, V. Fernandes, J.B. Pereira, M.D. Costa, S. Costa, V. Maximo, V. Macaulay, R. Rocha, D.C. Samuels (2009) American Journal of Human Genetics 84 (5) 628-640. PMC2681004.

 

 

The inheritance of pathogenic mitochondrial DNA mutations

L.M. Cree, D.C. Samuels, P.F. Chinnery (2009) Biochemica et Biophysica Acta – Molecular Basis of Disease 1792 (12), 1097-1102. PMC2785871.

 

Discrete stochastic simulation methods for chemically reacting systems

Y. Cao, D.C. Samuels (2009), Methods in Enzymology, 454, 115-140. PMID:19216925.

 

 

Detecting new neurodegenerative disease genes: Does phenotype accuracy limit the horizon?

D.C. Samuels, D.J. Burn, P.F. Chinnery (2009) Trends in Genetics 25 (11) 486-488. PMC2824109.

 

 

An Analysis of Enzyme Kinetics Data for Mitochondrial DNA Strand Termination by Nucleoside Reverse Transcriptase Inhibitors

K.V. Wendelsdorf, Z. Song, Y. Cao, D.C. Samuels (2009), PLOS Computational Biology 5(1) e1000261. PMC2603287.

 

 

The mitochondrial genome sequence and molecular phylogeny of the turkey, Meleagris gallopavo

X. Guan, P. Silva, O. Ho-Shing, K.B. Gyenai, J. Xu, T. Geng, Z. Tu, D.C. Samuels, O.E. Rhodes, E.J. Smith (2009), Animal Genetics 40(2): 134-141. PMC2664387.

 

 

2008

The Distribution of Mitochondrial DNA Heteroplasmy Due to Random Genetic Drift

P. Wonnapinij, P.F. Chinnery, D.C. Samuels (2008), American Journal of Human Genetics 83: 582-593. PubMed PMID:18976726; PMC2668051.

 

Evidence for variable selection pressures at a large secondary structure of the human mitochondrial DNA control region

F. Pereira, P. Soares, J. Carneiro, L. Pereira, M.B. Richards, D.C. Samuels, A. Amorim, (2008), Molecular Biology and Evolution 25(12): 2759-2770. PMID:18845547.

 

Pathogenic mitochondrial DNA mutations are common in the general public

H.R. Elliot, D.C. Samuels, J.A. Eden, C.L. Relton, P.F. Chinnery (2008). American Journal of Human Genetics 83: 254-260. PMC2495064.

 

What causes mitochondrial DNA deletions in human cells?

K.J. Krishnan, A.K. Reeve, D.C. Samuels, P.F. Chinnery, J.K. Blackwood, R.W. Taylor, S. Wanrooj, J.N. Spelbrink, R.N. Lightowlers, D.M. Turnbull (2008) Nature Genetics 40 (3): 275-279. PMID:18305478.

 

The evidence that the DNC (SLC25A19) is not the mitochondrial deoxyribonucleotide carrier

J. Kang and D.C. Samuels (2008), Mitochondrion 8: 103-108.PMID:18280798.

 

A reduction in the number of mitochondrial DNA molecules during embryogenesis explains the rapid segregation of genotypes

L.M. Cree, D.C. Samuels, S.C. de Sousa-Lopes, H.K. Rajasimha, P. Wonnapinij, J.R. Mann, H.H.M. Dahl, P.F. Chinnery (2008) Nature Genetics 40 (2): 249-254. PMID:18223651.

 

Selection against pathogenic mtDNA mutations in a stem cell population leads to the loss of the 3243A>G mutation in blood

H.K. Rajasimha, P.F. Chinnery, D.C. Samuels (2008), American Journal of Human Genetics 82: 333-343. PMC2427290.

 

2007

Normal levels of wild-type mitochondrial DNA maintain cytochrome c oxidase activity for two pathogenic mitochondrial DNA mutations but not for m.3243A -> G

S.E. Durham, D.C. Samuels, L.M. Cree, P.F. Chinnery (2007) American Journal of Human Genetics 81 (1): 189-195. PMC1950909.

 

Depletion of mitochondrial DNA in leucocytes harbouring the 3243A -> G mtDNA mutation

A. Pyle, R.W. Taylor, S.E. Durham, M. Deschauer, A.M. Schaefer, D.C. Samuels, P.F. Chinnery (2007), Journal of Medical Genetics 44 (1): 69-74. PMC2597915.

 

 

Computational models of antiviral toxicity

D.C. Samuels (2007), Current Opinion in Drug Discovery & Development 10 (1): 43-48. PMID:17265740.

 

 

2006

Mitochondrial AZT metabolism

D.C. Samuels (2006), IUBMB Life 58 (7): 403-408. PMID:16801215.

 

Is selection required for the accumulation of somatic mitochondrial DNA mutations in post-mitotic cells?

S.E. Durham, D.C. Samuels, P.F. Chinnery (2006) Neuromuscular Disorders 16 (6): 381-386. PMID:16684599.

 

 

The power to detect disease associations with mitochondrial DNA haplogroups

D.C. Samuels, A.D. Carothers, R. Horton, P.F. Chinnery (2006) American Journal of Human Genetics 78 (4): 713-720. PMC1424681.

 

2005

A computational model of mitochondrial AZT metabolism

P.C. Bradshaw, J.X. Li, D.C. Samuels (2005) Biochemical Journal 392: 363-373. PMC1316272.

 

Mitochondrial-encoded membrane protein transcripts are pyrimidine-rich while soluble protein transcripts and ribosomal RNA are purine-rich

P.C. Bradshaw, A. Rathi, D.C. Samuels (2005), BMC Genomics 6: Art. No. 136. PMC1262711.

 

Life span is related to the free energy of mitochondrial DNA

D.C. Samuels (2005), Mechanisms of Ageing and Development 126 (10): 1123-1129. PMID:15992863.

 

Mitochondrial DNA copy number threshold in mtDNA depletion myopathy,

S. Durham, E. Bonilla, D.C. Samuels, S. DiMauro, P.F. Chinnery (2005), Neurology 65 (3): 453-455. PMID:16087914

 

A computational model of mitochondrial deoxynucleotide metabolism and DNA replication

P.C. Bradshaw, D.C. Samuels (2005), The American Journal of Physiology: Cell Physiology 288: 989-1002. PMID:15634740.

 

 

2004

Two direct repeats cause most human mtDNA deletions

D.C. Samuels, E.A. Schon, P.F. Chinnery (2004), Trends in Genetics 20 (9): 393-398. PMID:15313545.

 

 

Mitochondrial DNA repeats constrain the life span of mammals

D.C. Samuels (2004), Trends in Genetics 20 (5): 226-229. PMID:15109774.

 

Scaling laws of vortex reconnections

C.F. Barenghi, D.C. Samuels (2004), Journal of Low Temperature Physics 136 (5-6): 281-293.

 

 

2003

A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate

D.C. Samuels, R.J. Boys, D.A. Henderson, P.F. Chinnery (2003), Nucleic Acids Research 31 (20): 6043-6052. PMC219467.

 

Mitochondrial DNA mutations in human colonic crypt stem cells

R.W. Taylor, M.J. Barron, G.M. Borthwick, A. Gospel, P.F. Chinnery, D.C. Samuels, G.A. Taylor, S.M. Plusa, S.J. Needham, L.C. Greaves, T.B.L. Kirkwood, D.M. Turnbull (2003) Journal of Clinical Investigation 112 (9): 1351-1360. PMC228466.

 

A model of the nuclear control of mitochondrial DNA replication,

G.J. Capps, D.C. Samuels, P.F. Chinnery (2003) Journal of Theoretical Biology 221 (4): 565-583. PMID:12713941.

 

Geometry and topology of superfluid turbulence

D.R. Poole, H. Scoffield, C.F. Barenghi, D.C. Samuels (2003), Journal of Low Temperature Physics 132 (1-2): 97-117.

 

Decay of superfluid turbulence via Kelvin-wave radiation

M. Leadbeater, D.C. Samuels, C.F. Barenghi, C.S. Adams (2003), Physical Review A 67 (1): #015601.

 

2002

Mitochondrial DNA mutations accumulate in ageing, cancer and mitochondrial disease: Is there a common mechanism?

P.F. Chinnery, D.C. Samuels, J.L. Elson, D.M. Turnbull (2002) Lancet 360 (9342): 1323-1325. PMID:12414225.

 

The length of cytochrome c oxidase negative segments in muscle fibres in patients with mtDNA myopathy

J.L. Elson, D.C. Samuels, M.A. Johnson, D.M. Turnbull, P.F. Chinnery (2002), Neuromuscular Disorders 12 (9): 858-864. PMID:12398838.

 

Polarization of superfluid turbulence

C.F. Barenghi, S. Hulton, D.C. Samuels (2002), Physical Review Letters 89 (27): #275301. PMID:12513214.

 

Evaporation of a packet of quantized vorticity

C.F. Barenghi, D.C. Samuels (2002), Physical Review Letters 89 (15): #155302. PMID:12365997.

 

Velocity spectra of superfluid turbulence

D. Kivotides, C.J. Vassilicos, D.C. Samuels, C.F. Barenghi (2002), Europhysics Letters 57 (6): 845-851.

 

 

Superfluid vortex reconnections

C.F. Barenghi, D.C. Samuels, D. Kivotides (2002), Journal of Low Temperature Physics 126 (1-2): 271-279.

 

2001

Random intracellular drift explains the clonal expansion of mitochondrial DNA mutations with age

J.L. Elson, D.C. Samuels, D.M. Turnbull, P.F. Chinnery (2001), American Journal of Human Genetics 68: 802-806. PMC1274494.

 

Random genetic drift determines the level of mutant mitochondrial DNA in human primary oocytes

D.T. Brown, D.C. Samuels, E.M. Michael, D.M. Turnbull, P.F. Chinnery (2001), American Journal of Human Genetics 68: 533-536. PMC1235288.

 

Quantum signature of superfluid turbulence

D. Kivotides, J.C. Vassilicos, C.F. Barenghi, M.A.I. Khan, D.C. Samuels (2001), Physical Review Letters 87 (27): #275302. PMID:11800889

 

A new interpretation of oscillating flow experiments in superfluid helium II

S.P. Godfrey, D.C. Samuels (2001), Journal of Low Temperature Physics 125 (1-2): 69-85.

 

Fractal dimension of superfluid turbulence

D. Kivotides, C.F. Barenghi, D.C. Samuels (2001), Physical Review Letters 87 (15): #155301. PubMed PMID:11580706.

 

How tangled is a tangle?

C.F. Barenghi, R.L. Ricca, D.C. Samuels (2001) Physica D 157 (3): 197-206.

 

Superfluid vortex reconnections at finite temperature

D. Kivotides, C.F. Barenghi, D.C. Samuels (2001), Europhysics Letters 54 (6): 774-778.

 

Linear stability of laminar plane Poiseuille flow of helium II under a nonuniform mutual friction forcing

S.P. Godfrey, D.C. Samuels, C.F. Barenghi (2001), Physics of Fluids 13 (4): 983-990.

 

Kelvin waves cascade in superfluid turbulence

D. Kivotides, J.C. Vassilicos, D.C. Samuels, C.F. Barenghi (2001), Physical Review Letters 86 (14): 3080-3083. PMID:11290112.

 

Sound emission due to superfluid vortex reconnections

M. Leadbeater, T. Winiecki, D.C. Samuels, C.F. Barenghi, C.S. Adams (2001), Physical Review Letters 86 (8): 1410-1413. PMID:11290155.

 

Formation and decay of vorticity in coupled helium-II flow

O.C. Idowu, K.L. Henderson, D.C. Samuels (2001), Physical Review B 63 (2): #024513.

 

2000

The inheritance of mitochondrial DNA heteroplasmy: random drift, selection or both?

P.F. Chinnery, D.R. Thorburn, D.C. Samuels, S.L. White, H.H.M. Dahl, D.M. Turnbull, R.N. Lightowlers, N. Howell (2000) Trends in Genetics 16: 500-505. PMID:11074292.

 

Can superfluid vortex lines excite normal fluid turbulence in He-4?

C.F. Barenghi, D. Kivotides, O.C. Idowu, D.C. Samuels (2000) Journal of Low Temperature Physics 121 (5-6): 377-386.

 

Triple vortex ring structure in superfluid helium II

D. Kivotides, C.F. Barenghi, D.C. Samuels (2000), Science 290 (5492): 777-779. PMID:11052935.

 

Equation for self-consistent superfluid vortex line dynamics

O.C. Idowu, D. Kivotides, C.F. Barenghi, D.C. Samuels, (2000) Journal of Low Temperature Physics 120 (3-4): 269-280.

 

Local normal fluid helium II flow due to mutual friction interaction with the superfluid

O.C. Idowu, A. Willis, C.F. Barenghi, D.C. Samuels (2000), Physical Review B 62 (5): 3409-3415.

 

Stable superfluid vortex filament structures in laminar boundary layer flow of helium II

S.P. Godfrey, D.C. Samuels (2000), Physical Review B 61 (6): 4190-4195.

 

1999

Relaxed replication of mtDNA: A model with implications for the expression of disease

P.F. Chinnery, D.C. Samuels (1999), American Journal of Human Genetics 64: 1158-1165. PMC1377840.

 

 

A damping length scale for superfluid turbulence

D.C. Samuels, D. Kivotides (1999) Physical Review Letters 83 (25): 5306-5309.

 

Evolution of vortex knots

R.L. Ricca, D.C. Samuels, C.F. Barenghi (1999), Journal of Fluid Mechanics 391: 29-44.

 

Self consistent decay of superfluid turbulence

C.F. Barenghi, D.C. Samuels (1999), Physical Review B 60 (2): 1252-1260.

 

1998

Instabilities during the dendritic and axonal development of neuronal form

H.G.E. Hentschel, D Samuels, A Fine (1998) Physica A – Statistical Mechanics and its Applications 254 (1-2): 46-64.

 

 

Vortex heating in superfluid helium at low temperatures

D.C. Samuels, C.F. Barenghi (1998), Physical Review Letters 81 (20): 4381-4383.

 

 

A finite length instability of vortex tubes

D.C. Samuels (1998), European Journal of Mechanics B – Fluids 17 (4): 587-594.

 

 

Quantized vortex knots

D.C. Samuels, C.F. Barenghi, R.L. Ricca (1998), Journal of Low Temperature Physics 110 (1-2): 509-514.

 

1997

The axon as a metabolic compartment: Protein degradation, transport, and the maximum length of an axon

K.E. Miller, D.C. Samuels (1997), Journal of Theoretical Biology 186: 373-379. PMID:9219672.

 

Superfluid vortex lines in a model of turbulent flow

C.F. Barenghi, D.C. Samuels, GH Bauer, RJ Donnelly (1997), Physics of Fluids 9 (9): 2631-2643.

 

 

1996

The origin of neuronal polarization: A model of axon formation

D.C. Samuels, H.G.E. Hentschel, A. Fine (1996) Philosophical Transactions of the Royal Society B 351: 1147-1156. PMID:8899865.

 

 

1994

Momentum statistics of interacting rotons

G.H. Bauer, D.C. Samuels, R.J. Donnelly (1994) Physica B 194 519-520

 

1993

Response of superfluid vortex filaments to concentrated normal-fluid vorticity

D.C. Samuels (1993), Physical Review B 47 (2): 1107-1110. PMID:10005596.

 

 

1992

Velocity matching and Poiseuille pipe-flow of superfluid-helium

D.C. Samuels (1992), Physical Review B 46 (18): 11714-11724. PMID:10003062.

 

 

1991

Motion of charged vortex rings in helium II

D.C. Samuels, R.J. Donnelly (1991), Physical Review Letters 67 (18): 2505-2508. PMID:10044443.

 

The effect of a Coriolis force on Taylor-Couette flow

R.J. Weiner, P.W. Hammer, C.E. Swanson, D.C. Samuels, R.J. Donnelly (1991), Journal of Statistical Physics 64 (5-6): 913-926.

 

 

1990

Dynamics of the interactions of rotons with quantized vortices in Helium-II

D.C. Samuels, R.J. Donnelly (1990), Physical Review Letters 65 (2): 187-190. PMID:10042575

 

 

Sideband instability and recurrence of Kelvin waves on vortex cores

D.C. Samuels, R.J. Donnelly (1990), Physical Review Letters 64 (12): 1385-1388. PMID:10041382.