David Samuels’ peer-reviewed publications in computational biology

Links to full text are in the journal names

 

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 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

 

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.

 

Analysis of enzyme kinetic data for mtDNA replication

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

 

Discrete stochastic simulation methods for chemically reacting systems

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

 

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.

 

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.

 

Computational models of antiviral toxicity

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

 

Mitochondrial AZT metabolism

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

 

A computational model of mitochondrial AZT metabolism

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

 

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.

 

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.

 

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.

 

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.

 

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.

 

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.

 

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.