ACADEMIC PAPERS

(click “PDF” for free, downloadable copy)

2024

• Smith DR. Espressogate. EMBO reports. In press. PDF
• Sanita Lima M*, Paschoal AR, Domingues DS, Smith DR. Long-read RNA-Seq for the discovery of long noncoding and antisense RNAs in plant organelles. Physiologia Plantarum. 176:e14418. PDF
• Sanita Lima M*, Domingues DS, Paschoal AR, Smith DR. Long-read RNA sequencing can probe organelle genome pervasive transcription. Briefings in Functional Genomics. In press. PDF (*PhD student)
• Smith DR. Your “out of the office” email is not fooling me. EMBO reports. 25:2511. PDF
• Huner NPA, Ivanov AG, Szyska-Mroz B, Savitch LV, Smith DR, Kata V. Photostasis and photosynthetic adaptation to polar life. Photosynthetic Research. 161:51. PDF
• Sanita Lima M, Lubbe FC, dos Santos SHD, Saruhashi S, Maglov JM, do Nascimento JM, Coulson SZ. 2024. Ecology, Ethology, and Evolution in the Anthropocene. Biology Open. 13:bio060175. PDF
  • This article and the conference it highlights was spearheaded and organized by Smith Lab PhD student M. Sanita Lima. 
• Sanita Lima M*, Paschoal AR, Domingues DS, Smith DR. Pervasive transcription of plant organelle genomes: functional noncoding transcriptomes? Trends in Plant Science. 29:626. PDF (*PhD student)
• Smith DR. Redefining meaning in science, research, and teaching. EMBO reports. 25:2147. PDF
• Hüner PA, Morgan-Kiss RM, Smith DR, Ivanov AG, Szyszka-Mroz B. The enigma of photopsychrophily and adaptation to polar habitats. CRC Press. In press.
• Smith DR. Finding value and beauty in obsolete scientific equipment. EMBO reports. 25:930. PDF

2023

• Smith DR. Things I wish I had done as a graduate student. EMBO reports. 24:e58291. PDF
• Smith DR. Science can be an anxiety-ridden road. It’s best to develop coping strategies early in the journey. EMBO reports. 24:e57882. PDF
• Fedder ZJF, Smith DR. In oceans, lakes, and ponds, living things can become what they eat. Frontiers for Young Minds. 11:1010245. PDF
• Hüner NPA, Szyszka-Mroz B, Ivanov AG, Kata V, Lye H, Smith DR. Photosynthetic adaptation and multicellularity in the Antarctic psychrophile Chlamydomonas priscuii. Algal Research. 74:103220. PDF
  • This article was written by an undergraduate volunteer (Zach Fedder) in the lab.
• Smith DR. When you lose your passion for science. EMBO reports. 24:e57262. PDF
  • This essay touches upon my recent struggles with cancer. 
• Zhang X, Hu Y, Smith DR. HSDatabase – a database of highly similar duplicate genes from plants, animals, and algae. Oxford Database. baac086. PDF

2022

• Cvetkovska M, Vakulenko G, Smith DR, Zhang X, Hüner NPA. Temperature stress in psychrophilic green microalgae: Minireview. Physiologia Plantarum 174:e13811. PDF
• DeShaw AE, Figueroa-Martinez F, Pröschold T, Lorenz M, Nedelcu AM, Smith DR, Reyes-Prieto A. The plastid genomes of Hyalomonas oviformis and Hyalogonium fusiforme evolved dissimilar architectures after the loss of photosynthesis. Plant Direct. 6:e454. PDF
• Zhang X*, Smith DR. An overview of online resources for intra-species detection of gene duplications. Frontiers in Genetics. 13:1012788. PDF (*PhD student)
  • This article is part of the research topic “Insights in Computational Genomics: 2022.
• Smith DR. After 2 years of a pandemic students are struggling to find strong reference letters. EMBO reports. 23:e55780. PDF
• Xiang QP, Tang J, Yu J, Smith DR, Zhu Y, Wang YR, Kang JS, Yang J, Zhang XC. The evolution of extremely diverged plastomes in Selaginellaceae (lycophyte) is driven by repeat patterns and the underlying DNA maintenance machinery. The Plant Journal. 111:768-784. PDF
• Smith DR, Leung A^#, Zhang X^*, Cvetkovska M, Morgan-Kiss R, Hüner NPA. An Antarctic alga that can survive the extreme cold. Frontiers in Young Minds. 10:740838. PDF (^#undergraduate,  *PhD student)
• Smith DR. The underappreciated art of creating publication-quality figures. EMBO reports. 23:e55114. PDF 
• Smith DR. A species by any other name would sound as sweet. EMBO reports. 23:e54643. PDF
• Smith DR. Genome Evolution: Minicircular mtDNA and unusual heteroplasty in a parasitic plant. Current Biology. 32:PR86-PR89. PDF
• Cvetkovska M, Zhang X*, Vakulenko G, Benzaquen S, Szyszka-Mroz B, Malczewski N, Smith DR, Hüner NPA. A Constitutive stress response is a result of low temperature growth in the Antarctic green alga Chlamydomonas sp. UWO241. Plant, Cell & Environment. 45:156-177. PDF (*PhD student)
• Smith DR. The genome paper is dead, long live the genome paper! EMBO reports. 23:e54434. PDF
• Torson AS, Hicks AMA, Baragar CE, Smith DR, Sinclair BJ. The mitochondrial genome of two Gryllus crickets (Grylloidea: Gryllidae) via RNA-seq. Mitochondrial DNA Part B: Resources. 7:106-107. PDF
• Hüner NPA, Smith DR, Cvetkovska M, Zhang X^*, Ivanov A, Szyszka-Mroz B, Morgan-Kiss R. Photosynthetic adaptation to polar life: photopsychrophily and psychrotolerance as emergent properties. Journal of Plant Physiology. 268:153557. PDF (*PhD student)

2021

• Zhang X*, Hu Y, Smith DR. HSDFinder: a BLAST-based strategy for identifying highly similar duplicated genes in eukaryotic genomes. Frontiers in Bioinformatics. 1:803176. PDF (*PhD Student)
• Eldred L*, Thorn G, Smith DR. Simple matching using the QIIME 2 and RDP reveals misidentified sequences and an underrepresentation of fungi in reference datasets. Frontiers in Genetics. 12: 768473. PDF (*Undergraduate)
• Thompson SRL*, Lee DK^#, Lachance MA, Smith DR. Mutational effects of self-splicing introns on the mitochondrial genomes of Metschnikowia yeasts. Frontiers in Genetics. 12: 785218. PDF (*Undergraduate, ^#MSc student)
• Smith DR. Confessions of a microscope hoarder. EMBO reports. 22: e54024. PDF
• Zhang Xi*, Yining H, Smith DR. Protocol for using NoBadWordsCombiner to merge and minimize ‘bad words’ from BLAST hits against multiple eukaryotic gene annotation databases. STAR Protocols (by Cell Press). 2: 100888. PDF (*PhD Student)
• Smith DR. The human touch. EMBO reports. e53789. PDF
• Zhang X^*, Hu Yining, Smith DR. Protocol for HSDFinder: identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes. STAR Protocols (by Cell Press). 2: 100619. PDF (*PhD student)
• Smith DR. Alcodemia: are we training our students to be great thinkers or great drinkers? EMBO reports. 22: e53362. PDF
• Smith DR. University campuses need people in them. EMBO reports. 22: e52591. PDF
• Kayal E, Smith DR. Is the dinoflagellate Amoebophrya really missing a mtDNA? Molecular Biology and Evolution. 38: 2493–2496. PDF
• Zhang X*, Cvetkovska M, Morgan-Kiss R, Hüner NPA, Smith DR. Draft genome sequence of the Antarctic green alga Chlamydomonas sp. UWO241. iScience. 24: 102084. PDF (*PhD student)
  • This article represents the first complete nuclear genome sequence from an Antarctic lake.
• Smith DR. Do scientists read enough fiction? EMBO reports. 22: e52205. PDF
  • Please see associated correspondence to this article: Porter JD. A role for fiction in science. EMBO reports. e52614. PDF
  • This article generated significant discussion online (click for details).
• Smith DR. A short guide to genetic data mining. EMBO reports. 22: e51845. PDF
• Smith DR, Craig RJ. Does mitochondrial DNA replication in Chlamydomonas require a reverse transcriptase? New Phytologist. 229: 1192-1195. PDF

2020

• Smith DR. Do you miss the conference circuit? I surely don’t. EMBO reports. 21: e51565. PDF
• Smith DR. Depositing annotated sequences in GenBank: there needs to be a better way. Briefings in Functional Genomics. 19:337-338. PDF
• Smith DR. Revisiting Ceriantharia (Anthozoa) mitochondrial genomes: casting doubts about their structure and size. Genome Biology and Evolution. 12:1440-1443. PDF
• Lee DK*, Hsiang T, Lachance MA, Smith DR. The strange mitochondrial genomes of Metschnikowia yeasts. Current Biology. 30:R800-R801. PDF (*MSc student)
• Smith DR. Is sabbatical a dirty word? EMBO reports. 21:e50886. PDF
• Smith DR. Common repeat elements in the mitochondrial and plastid genomes of green algae. Frontiers in Genetics. 11:465. PDF  
  • This article is part of the Frontiers special research topic: Evolution of Mitochondrial Genomes.
• Smith DR. Academic street smarts: be vigilant of fraudsters. EMBO reports. 21:e50365. PDF
• Smith DR. Can green algal plastid genome size be explained by DNA repair mechanisms? Genome Biology and Evolution. 12:3797-3802. PDF
• Smith DR. Unparalleled variation in RNA editing among Selaginella plastomes. Plant Physiology. 182:12-14. PDF
  • This article is part of a special focus issue on RNA biology in plants. See editorial here.

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2019

• Smith DR. Revisiting published genomes with fresh eyes and new data. EMBO reports. 20:e49482. PDF
• Smith DR, Cvetkovska M, Hüner NPA, Morgan-Kiss R. 2019. Presence and absence of light-independent chlorophyll biosynthesis among Chlamydomonas green algae in an ice-covered Antarctic lake. Communicative & Integrative Biology. 12:148-150. PDF
• Zhang X*, Bauman N, Brown R, Richardson TH, Akella S, Hann E, Morey R, Smith DR. 2019. The mitochondrial and chloroplast genomes of the green alga Haematococcus are largely made up of nearly identical repetitive sequences. Current Biology. 25:R736-R737. PDF (*PhD student)
• Szyszka-Mroz B, Cvetkovska M, Ivanov AG, Smith DR, Possmayer M, Maxwell DP, Hüner NPA. Cold-adapted protein kinases and thylakoid remodelling impact energy distribution in an Antarctic psychrophile. Plant Physiology. 180:1291-1309. PDF
• Grisdale CJ, Smith DR, Archibald JM. Relative mutation rates in nucleomorph-bearing algae. Genome Biology and Evolution. 11:1045–1053. PDF
• Smith DR (2019) Evolution: A plant plastid genome that has forsaken guanine and cytosine. Current Biology. 29:R99-R101. PDF
• Cvetkovska M, Orgnero S, Hüner NPA, Smith DR (2019) The enigmatic loss of light-independent chlorophyll biosynthesis from an Antarctic green alga in a light-limited environment. New Phytologist. 222:651–656. PDF

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2018

• Smith DR (2018) Haematococcus lacustris: the makings of a giant-sized chloroplast genome. AoB Plants. 10:ply058. PDF
• Smith DR (2018) Is it time to put a humidifier in the dry domain of writing scientific papers. EMBO reports. e46909. PDF
• Gaouda H*, Hamaji T, Yamamoto K, Kawai-Toyooka H, Suzuki M, Noguchi H,Minakuchi Y, Toyoda A, Fujiyama A, Nozaki H, Smith DR (2018) Exploring the limits and causes of plastid genome expansion in volvocine green algae. Genome Biology and Evolution. 10:2248-2254. PDF (*MSc student)
• Smith DR (2018) Bringing bioinformatics to the scientific masses. EMBO reports. 19:e46262. PDF
• Cvetkovska M, Szyszka-Mroz B, Possmayer M, Pittock P, Lajoie G, Smith DR, Hüner NPA (2018) Characterization of photosynthetic ferredoxin from the Antarctic algal Chlamydomonas sp. UWO241 reveals novel features of cold adaptation. New Phytologist. 219: 588-604. PDF 
• Smith DR (2018) Plastid genomes hit the big time. New Phytologist. 219: 491-495. PDF
• Su Y, Willis L, Rehmann L, Smith DR, Jeffries T (2018) Spathaspora passalidarum selected for resistance to AFEX hydrolysate shows decreased cell yield. FEMS Yeast Research. 18:foy011. PDF 
• Smith DR (2018) Attention, attention: your most valuable scientific assets are under attack. EMBO reports. 19:e45684. PDF 
• Smith DR (2018) The Frankenthesis: this stitched-together monster is alive and coming to a campus near you. EMBO reports. 19:10-12 PDF
• Smith DR (2018) Lost in the light: genome evolution in colourless plastids. Advances in Botanical Research. 85:29-53. PDF

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2017

• Smith DR (2017) Evolution: In chloroplast genomes, anything goes. Current Biology. 27:R1305–07. PDF
• Smith DR (2017) Does cell size impact chloroplast genome size? Frontiers in Plant Science. 8:2116. PDF
• Sanitá Lima M*, Smith DR (2017) Pervasive transcription of mitochondrial, plastid, and nucleomorph genomes across diverse plastid-bearing species. Genome Biology and Evolution. 9:2650-57. PDF (*MSc student)
• Sanitá Lima M*, Smith DR (2017) Don’t just dump your data and run. EMBO reports. 18:2087-89. PDF (*MSc student)
• Sanitá Lima M*, Smith DR (2017) Pervasive, genome-wide transcription in the organelle genomes of diverse plastid-bearing protists. G3: Genes | Genomes | Genetics. 7:3789-96. PDF (*MSc student)
• Smith DR (2017) Let there be light: a contemporary primer on primary plastid endosymbiosis. Advances in Botanical Research. 84:31-56. PDF
• Hamaji T, Kawai-Toyooka H, Toyoda A, Minakuchi Y, Suzuki M, Fujiyama A, Nozaki H*, Smith DR* (2017) Multiple independent changes in mitochondrial genome conformation in chlamydomonadalean algae. Genome Biology and Evolution. 9:993-99. PDF (*co-corresponding authors)
• Figueroa-Martinez F, Nedelcu A, Reyes-Prieto A*, Smith DR* (2017) The plastid genomes of nonphotosynthetic algae are not so small after all. Communicative & Integrative Biology. 10:e1283080. PDF (*co-corresponding authors)
• Smith DR (2017) The plant Lophophytum pilfers mitochondrial genes from the species it parasitizes. The Scientist. 27:2. PDF
• Smith DR (2017) Confessions of a science blogaholic: highs, lows, and increasing liabilities. Frontiers in Communication. 1:15. PDF
• Figueroa-Martinez F, Nedelcu AM, Smith DR*, Reyes-Prieto A* (2017) The plastid genome of Polytoma uvella is the largest known among colorless algae and plants and reflects contrasting evolutionary paths to nonphotosynthetic lifestyles. Plant Physiology. 173:932-43. PDF (*co-corresponding authors)
• Smith DR (2017) More than ever, scientists need to engage with the public: the stakes are high and they may be for keeps. EMBO reports. 18:185-6. PDF
• Cvetkovska M, Hüner NPA, Smith DR (2017) Chilling out: the evolution and diversification of psychrophilic algae, with a focus on Chlamydomonadales. Polar Biology. 40:1169-84. PDF
• Smith DR, Sanitá Lima M* (2017) Unraveling chloroplast transcriptomes with ChloroSeq, an organelle RNA-Seq bioinformatics pipeline. Briefings in Bioinformatics. 18:1012-16. PDF (*MSc student)
• Smith DR (2017) Goodbye genome paper, hello genome report: the increasing popularity of “genome announcements” and their impact on science. Briefings in Functional Genomics. 16:156-62. PDF
  • This article was recommended by F1000. PDF

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 2016

• Smith DR (2016) A walk in the park: Is Pokémon Go foreshadowing the future of biodiversity research and scientific outreach? EMBO reports. 17:1506–9. PDF
• Smith DR (2016) One scientist’s struggle to be a better writer, and a plea for undergraduate science-writing engagement. Science Communication. 38:666–74. PDF
  • This article was translated into Chinese (PDF) and published in the journal Science Writer in 2017.  
• Sanita Lima M¹, Woods LC,Cartwright MW², Smith DR (2016) The (in)complete organelle genome: exploring the use and non-use of available technologies for characterizing mitochondrial and plastid chromosomes. Molecular Ecology Resources. 16:1279–86. PDF (1: MSc student, 2: Honours student)
• Smith DR (2016) The mutational hazard hypothesis of organelle genome evolution: ten years on. Molecular Ecology. 25:3769–3775. PDF
• Featherston F, Arakaki Y, Nozaki H, Durand PM, Smith DR (2016) Inflated organelle genomes and a circular-mapping mtDNA likely existed at the origin of coloniality in volvocine green algae. European Journal of Phycology. 51:369–77. PDF
• Smith DR, Keeling PJ (2016) Protists and the wild, wild west of gene expression: new frontiers, lawlessness, and misfits. Annual Review of Microbiology. 70:161–78. PDF 
• Hanschen, et al. (2016) The Gonium pectorale genome demonstrates co-option of cell cycle regulation during the evolution of multicellularity. Nature Communications. 7:11370. PDF
  • See press coverage in EurekaAlert!, the Washington Post, and the NewHistorian.
• Smith DR (2016) Will publons popularize the scientific peer-review process? BioScience. 66:265–6. PDF
• Tian Y*, Smith DR (2016) Recovering complete mitochondrial genome sequences from RNA-Seq: a case study of Polytomella non-photosynthetic green algae. Molecular Phylogenetics and Evolution. 98:57–62. PDF (*Honours student.)
  • See commentary by RNA-Seq Blog.
• Possmayer M, Gupta RK, Szyska-Mroz B, Maxwell DP, Lachance MA, Hüner NPA, Smith DR (2016) Resolving the phylogenetic position of Chlamydomonas sp. UWO 241 (Chlorophyceae) with nuclear and organelle DNA sequences. Journal of Phycology. 52:305–10. PDF
• Smith DR (2016) Are you failing at scientific social media? EMBO reports. 17:123–4. PDF
• Smith DR (2016) The past, present, and future of mitochondrial genomics: have we sequenced enough mtDNAs? Briefings in Functional Genomics. 15:47–54. PDF
  • See opinion piece in The Scientist that accompanies this article.
  • See comment by Rob DeSale in Briefings in Functional Genomics. PDF
• Asmail SR*, Smith DR (2016) Retention, erosion, and loss of the carotenoid biosynthetic pathway in the nonphotosynthetic green algal genus Polytomella. New Phytologist. 209:899–903. PDF (*MSc student in the Smith Lab.)

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2015

• Yan D, et al. (2015) Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae. Scientific Reports. 5:14465. PDF
• Smith DR (2015) Broadening the definition of a bioinformatician. Frontiers in Genetics. 6:258. PDF
• Smith DR (2015) Mutation rates in plastid genomes: they are lower than you might think. Genome Biology and Evolution. 7:1227–34. PDF
• Smith DR, Keeling PJ (2015) Mitochondrial and plastid genome architecture: reoccurring themes, but significant differences at the extremes. Proceedings of the National Academy of Sciences USA. 112:10177–84. PDF 
  • See the PNAS Sackler Colloquium seminar that accompanies this article. 
  • This research was highlighted in the 31 Oct 2014 issue of Science (PDF).
  • This article was recommended by F1000.
• Del Vasto M*, Figueroa-Martinez F, Featherston J, Gonzalez MA, Reyes-Prieto A, Durrand PM, Smith DR (2015) Massive and widespread organelle genomic expansion in the green algal genus Dunaliella. Genome Biology and Evolution. 7:656–63. PDF (*MSc student in the Smith Lab) 
• Figueroa-Martinez F, Nedelcu AM, Smith DR*, Reyes-Prieto A* (2015) When the lights go out: the evolutionary fate of free-living colourless green algae. New Phytologist. 206:972–82. PDF (*co-corresponding authors)
• Ajoge HO*, Olonitola SO, Smith DR (2015) Soil-transmitted helminths are a serious but understudied health concern in South Africa, requiring immediate attention from the scientific community. F1000Research. 3:209. PDF (*Visiting scholar in Smith Lab.)
• Smith DR (2015) Buying in to bioinformatics: an introduction to commercial sequence analysis software. Briefings in Bioinformatics. 16:700–9. PDF 
  • See opinion piece in The Scientist that accompanies this article.
• Smith DR (2015) The outsourcing and commercialization of science. EMBO Reports. 16:14–6. PDF

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2014

• Smith DR, Jackson CJ, Reyes-Prieto A (2014) Nucleotide substitution analyses of the glaucophyte Cyanophora suggest an ancestrally lower mutation rate in plastid vs mitochondrial DNA for the Archaeplastida. Molecular Phylogenetics and Evolution. 79:380–384. PDF
• Smith DR, Asmail SR (2014) Next-generation sequencing data suggest that certain nonphotosynthetic green plants have lost their plastid genomes. New Phytologist. 204:7–11. PDF (*MSc student in the Smith Lab.)
  
• Keeling PJ, (75 other authors, including Smith DR), Worden AZ (2014) The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biology. 12:e1001889. PDF 
  • See opinion piece in The Scientist that highlights this research.
• Smith DR (2014) Last-gen nostalgia: a lighthearted rant and reflection on genome sequencing culture. Frontiers in Genetics. 5:146. PDF 
  • See blog post by science writer and academic John Hawks highlighting this article. Based on Altmetric, this is the 6th highest scoring article ever published in Frontiers in Genetics.
• Smith DR, Vinogradov SN, Hoogewijs D (2014) Hemoglobins in the genome of the cryptomonad Guillardia theta. Biology Direct. 9:7. PDF
• Smith DR, Lee RW (2014) A plastid without a genome: evidence from the nonphotosynthetic green alga Polytomella. Plant Physiology. 164:1812–9. PDF 
  • This article was covered by various news media, including Science and The Scientist. It was also the focus of a highlight article in Nature Reviews Genetics: Jones B. 2014, 15:288. PDF
    
• Smith DR (2014) Mitochondrion-to-plastid DNA transfer: it happens. New Phytologist. 202:736–8. PDF
  
• Smith DR, Arrigo KR, Alderkamp AC, Allen AE (2014) Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae. Molecular Phylogenetics and Evolution. 71:36–40. PDF
• Smith DR (2014) Volvox, rolling out from under the shadow of Chlamydomonas. Journal of Heredity. 105:143–144. PDF

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2013

• Smith DR (2013) Are we divorced from the species we study? F1000Research. 2:254. PDF *This article was a front-page featured paper on the F1000Research website for the week of 10–14 Dec 2013, and included a comment from the journal’s editor.
• Smith DR (2013) The battle for user-friendly bioinformatics. Frontiers in Genetics. 4:187. PDF
• Smith DR, Hua J, Archibald JM, Lee RW (2013) Palindromic genes in the linear mitochondrial genome of the nonphotosynthetic green alga Polytomella magna. Genome Biology and Evolution. 5:1661–7. PDF
• Smith DR, James ER (2013) What’s in a name? A lot if you’re a little known microbe. BioScience. 63:791–2. PDF 
  • This article was highlighted by Smithsonian.com “Why do we keep naming new species after characters in pop culture?” 5 Nov 2013. 
• Vinogradov SN, Bailly X, Smith DR, Tinajero-Trejo M, Poole RK, Hoogewijs D (2013) Microbial eukaryote globins. Advances in Microbial Physiology. 63:391–446. PDF
• Smith DR (2013) Death of the genome paper. Frontiers in Genetics. 4:72. PDF *Based on Altmetric, this is among highest scoring article ever published in Frontiers in Genetics.
  
• Smith DR, Keeling PJ (2013) Gene conversion shapes linear mitochondrial genome architecture. Genome Biology and Evolution. 5:905–12. PDF
• Smith DR (2013) Steal my sunshine. The Scientist. 27:34–40.
• Hamaji T, Smith DR, Noguchi H, Toyoda A, Suzuki M, Kawai-Toyooka H, Fujiyama A, Nishi A, Marriage T, Olson BJSC, Nozaki H (2013) Mitochondrial and plastid genomes of the colonial green alga Gonium pectorale give insights into the origins of organelle DNA architecture within the Volvocales. PLoS ONE. 8:e57177. PDF
• Smith DR, Hamaji T, Olson BJSC, Durand PM, Ferris P, Michod RE, Nozaki H, Featherston J, Keeling PJ (2013) Organelle genome complexity scales positively with organism size in volvocine green algae. Molecular Biology and Evolution. 30:793–7. PDF
• Pombert JF, Xu J, Smith DR, Heiman D, Young S, Cuomo C, Weiss LM, Keeling PJ (2013) Complete genome sequences from three genetically distinct strains reveal a high intra-species genetic diversity in the microsporidian Encephalitozoon cuniculi. Eukaryotic Cell. 12:503–11. PDF
• Smith DR (2013) RNA-Seq data: a goldmine for organelle research. Briefings in Functional Genomics. 12:454–6. PDF

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2012

• Crosby K, Smith DR (2012) Does the mode of plastid inheritance influence plastid genome architecture? PLoS ONE. 7:e46260. PDF
• Smith DR (2012) Updating our view of organelle genome nucleotide landscape. Frontiers in Genetics. 3:175. PDF
• Smith DR (2012) Making your GenBank entry count. Frontiers in Genetics. 3:123. PDF
• Smith DR, Hua J, Lee RW, Keeling PJ (2012) Relative rates of evolution among the three genetic compartments of the red alga Porphyra differ from those of green plants and do not correlate with genome architecture. Molecular Phylogenetics and Evolution. 65:339–44. PDF
• Smith DR (2012) Not seeing the genomes for the DNA. Briefings in Functional Genomics. 11:289–90. PDF
• Smith DR, Keeling PJ (2012) Twenty-fold difference in evolutionary rates between the mitochondrial and plastid genomes of species with secondary red plastids. Journal of Eukaryotic Microbiology. 59:181–4. PDF
• Smith DR, Kayal E, Yanagihara AA, Collins AG, Pirro S, Keeling PJ (2012) First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented, linear architecture and insights into telomere evolution. Genome Biology and Evolution. 4:52–8. PDF
• Leliaert F, Smith DR, Moreau H, Herron M, Verbruggen H, Delwiche CF, De Clerk O (2012) Phylogeny and molecular evolution of the green algae. Critical Reviews in Plant Sciences. 31:1–46. PDF
• Hua J, Smith DR, Borza T, Lee RW (2012) Similar relative mutation rates in the three genetic compartments of Mesostigma and Chlamydomonas. Protist. 163:105–15. PDF

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2011

• Smith DR, Burki F, Yamada T, Grimwood J, Grigoriev IV, Van Etten JL, Keeling PJ (2011) The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape. PLoS ONE. 6:e23624. PDF
• Smith DR (2011) Extending the limited transfer window hypothesis to inter-organelle DNA migration. Genome Biology and Evolution. 3:743–8. PDF
• Smith DR, Lee RW (2011) Nucleotide diversity in the colorless green alga Polytomella parva (Chlorophyceae, Chlorophyta): high for the mitochondrial telomeres, surprisingly low everywhere else. Journal of Eukaryotic Microbiology. 58:471–3. PDF
• Smith DR, Crosby K, Lee RW (2011) Correlation between nuclear plastid DNA abundance and plastid number supports the limited transfer window hypothesis. Genome Biology and Evolution. 3:365–71. PDF 
  • This article was highlighted by the journal in a commentary article by science writer Nick Lane: (2011) Plastids, genomes, and the probability of gene transfer. Genome Biology and Evolution. 3:372–4. PDF 

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2010

• Smith DR, Hua J, Lee RW (2010) Evolution of linear mitochondrial DNA in three known lineages of Polytomella. Current Genetics. 56:427–38. PDF
• Smith DR, Lee RW, Cushman JC, Magnuson JK, Tran D, Polle JEW (2010) The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA. BMC Plant Biology. 10:83. PDF
• Smith DR, Lee RW (2010) Low nucleotide diversity in the organelle and nuclear genomes of Volvox carteri provides support for the mutational-hazard hypothesis. Molecular Biology and Evolution. 27:2244–56. PDF

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2009

• Smith DR (2009) Unparalleled GC content in the plastid DNA of Selaginella. Plant Molecular Biology. 71:627–39. PDF
• Smith DR, Lee RW (2009) Nucleotide diversity of the Chlamydomonas reinhardtii plastid genome: addressing the mutational-hazard hypothesis. BMC Evolutionary Biology. 9:120. PDF
• Smith DR, Lee RW (2009) The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA. BMC Genomics. 10:132. PDF

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2008

• Smith DR, Lee RW (2008) Nucleotide diversity in the mitochondrial and nuclear compartments of Chlamydomonas reinhardtii: investigating the origins of genome architecture. BMC Evolutionary Biology. 8:156. PDF
• Smith DR, Lee RW (2008) Mitochondrial genome of the colorless green alga Polytomella capuana: a linear molecule with an unprecedented GC content. Molecular Biology and Evolution. 25:487–96. PDF

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2007

• Smith DR, Snyder M (2007) Complete mitochondrial DNA sequence of the scallop Placopecten magellanicus: evidence of transposition leading to an uncharacteristically large mitochondrial genome. Journal of Molecular Evolution. 65:380–91. PDF