Stephen A. Smith - Publications

Affiliations: 
University of Michigan, Ann Arbor, Ann Arbor, MI 
Area:
Evolutionary Biology, Phylogenetics, Phyloinformatics, Plant evolution, Transcriptomics

47 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
2020 Singhal S, Colston TJ, Grundler MR, Smith SA, Costa GC, Colli GR, Moritz C, Pyron RA, Rabosky DL. Congruence and conflict in the higher-level phylogenetics of squamate reptiles: an expanded phylogenomic perspective. Systematic Biology. PMID 32681800 DOI: 10.1093/Sysbio/Syaa054  0.6
2018 Pease JB, Brown JW, Walker JF, Hinchliff CE, Smith SA. Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life. American Journal of Botany. 105: 385-403. PMID 29746719 DOI: 10.1002/Ajb2.1016  1
2018 Eiserhardt WL, Antonelli A, Bennett DJ, Botigué LR, Burleigh JG, Dodsworth S, Enquist BJ, Forest F, Kim JT, Kozlov AM, Leitch IJ, Maitner BS, Mirarab S, Piel WH, Pérez-Escobar OA, ... ... Smith SA, et al. A roadmap for global synthesis of the plant tree of life. American Journal of Botany. PMID 29603138 DOI: 10.1002/Ajb2.1041  0.56
2015 Zapata F, Goetz FE, Smith SA, Howison M, Siebert S, Church SH, Sanders SM, Ames CL, McFadden CS, France SC, Daly M, Collins AG, Haddock SH, Dunn CW, Cartwright P. Phylogenomic Analyses Support Traditional Relationships within Cnidaria. Plos One. 10: e0139068. PMID 26465609 DOI: 10.1371/Journal.Pone.0139068  1
2015 Hinchliff CE, Smith SA, Allman JF, Burleigh JG, Chaudhary R, Coghill LM, Crandall KA, Deng J, Drew BT, Gazis R, Gude K, Hibbett DS, Katz LA, Laughinghouse HD, McTavish EJ, et al. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Sciences of the United States of America. PMID 26385966 DOI: 10.1073/Pnas.1423041112  1
2015 Brockington SF, Yang Y, Gandia-Herrero F, Covshoff S, Hibberd JM, Sage RF, Wong GK, Moore MJ, Smith SA. Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales. The New Phytologist. PMID 25966996 DOI: 10.1111/Nph.13441  1
2015 McTavish EJ, Hinchliff CE, Allman JF, Brown JW, Cranston KA, Holder MT, Rees JA, Smith SA. Phylesystem: a git-based data store for community-curated phylogenetic estimates. Bioinformatics (Oxford, England). PMID 25940563 DOI: 10.1093/Bioinformatics/Btv276  1
2015 Yang Y, Moore MJ, Brockington SF, Soltis DE, Wong GK, Carpenter EJ, Zhang Y, Chen L, Yan Z, Xie Y, Sage RF, Covshoff S, Hibberd JM, Nelson MN, Smith SA. Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing. Molecular Biology and Evolution. 32: 2001-14. PMID 25837578 DOI: 10.1093/Molbev/Msv081  1
2015 Smith SA, Moore MJ, Brown JW, Yang Y. Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants Bmc Evolutionary Biology. 15. DOI: 10.1186/s12862-015-0423-0  1
2014 Yang Y, Smith SA. Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Molecular Biology and Evolution. 31: 3081-92. PMID 25158799 DOI: 10.1093/Molbev/Msu245  1
2014 Hinchliff CE, Smith SA. Some limitations of public sequence data for phylogenetic inference (in plants). Plos One. 9: e98986. PMID 24999823 DOI: 10.1371/Journal.Pone.0098986  1
2014 Izquierdo-Carrasco F, Cazes J, Smith SA, Stamatakis A. PUmPER: phylogenies updated perpetually. Bioinformatics (Oxford, England). 30: 1476-7. PMID 24478338 DOI: 10.1093/Bioinformatics/Btu053  1
2014 Drew BT, Ruhfel BR, Smith SA, Moore MJ, Briggs BG, Gitzendanner MA, Soltis PS, Soltis DE. Another look at the root of the angiosperms reveals a familiar tale. Systematic Biology. 63: 368-82. PMID 24391149 DOI: 10.1093/Sysbio/Syt108  1
2014 Zanne AE, Tank DC, Cornwell WK, Eastman JM, Smith SA, FitzJohn RG, McGlinn DJ, O'Meara BC, Moles AT, Reich PB, Royer DL, Soltis DE, Stevens PF, Westoby M, Wright IJ, et al. Three keys to the radiation of angiosperms into freezing environments. Nature. 506: 89-92. PMID 24362564 DOI: 10.1038/Nature12872  0.96
2014 Cornwell WK, Westoby M, Falster DS, Fitzjohn RG, O'Meara BC, Pennell MW, McGlinn DJ, Eastman JM, Moles AT, Reich PB, Tank DC, Wright IJ, Aarssen L, Beaulieu JM, Kooyman RM, ... ... Smith SA, et al. Functional distinctiveness of major plant lineages Journal of Ecology. 102: 345-356. DOI: 10.1111/1365-2745.12208  1
2013 Ryan JF, Pang K, Schnitzler CE, Nguyen AD, Moreland RT, Simmons DK, Koch BJ, Francis WR, Havlak P, Smith SA, Putnam NH, Haddock SH, Dunn CW, Wolfsberg TG, et al. The genome of the ctenophore Mnemiopsis leidyi and its implications for cell type evolution. Science (New York, N.Y.). 342: 1242592. PMID 24337300 DOI: 10.1126/Science.1242592  1
2013 Smith SA, Brown JW, Hinchliff CE. Analyzing and synthesizing phylogenies using tree alignment graphs. Plos Computational Biology. 9: e1003223. PMID 24086118 DOI: 10.1371/Journal.Pcbi.1003223  1
2013 Rabosky DL, Santini F, Eastman J, Smith SA, Sidlauskas B, Chang J, Alfaro ME. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature Communications. 4: 1958. PMID 23739623 DOI: 10.1038/Ncomms2958  1
2013 Yang Y, Smith SA. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics. Bmc Genomics. 14: 328. PMID 23672450 DOI: 10.1186/1471-2164-14-328  1
2012 Smith SA, O'Meara BC. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics (Oxford, England). 28: 2689-90. PMID 22908216 DOI: 10.1093/Bioinformatics/Bts492  1
2012 Stamatakis A, Aberer AJ, Goll C, Smith SA, Berger SA, Izquierdo-Carrasco F. RAxML-Light: a tool for computing terabyte phylogenies. Bioinformatics (Oxford, England). 28: 2064-6. PMID 22628519 DOI: 10.1093/Bioinformatics/Bts309  1
2012 Aliscioni S, Bell HL, Besnard G, Christin PA, Columbus JT, Duvall MR, Edwards EJ, Giussani L, Hasenstab-Lehman K, Hilu KW, Hodkinson TR, Ingram AL, Kellogg EA, Mashayekhi S, Morrone O, ... ... Smith SA, et al. New grass phylogeny resolves deep evolutionary relationships and discovers C 4 origins New Phytologist. 193: 304-312. PMID 22115274 DOI: 10.1111/j.1469-8137.2011.03972.x  1
2011 Izquierdo-Carrasco F, Smith SA, Stamatakis A. Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. Bmc Bioinformatics. 12: 470. PMID 22165866 DOI: 10.1186/1471-2105-12-470  1
2011 Smith SA, Wilson NG, Goetz FE, Feehery C, Andrade SC, Rouse GW, Giribet G, Dunn CW. Resolving the evolutionary relationships of molluscs with phylogenomic tools. Nature. 480: 364-7. PMID 22031330 DOI: 10.1038/Nature10526  1
2011 Siebert S, Robinson MD, Tintori SC, Goetz F, Helm RR, Smith SA, Shaner N, Haddock SH, Dunn CW. Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows. Plos One. 6: e22953. PMID 21829563 DOI: 10.1371/Journal.Pone.0022953  1
2011 Soltis DE, Smith SA, Cellinese N, Wurdack KJ, Tank DC, Brockington SF, Refulio-Rodriguez NF, Walker JB, Moore MJ, Carlsward BS, Bell CD, Latvis M, Crawley S, Black C, Diouf D, et al. Angiosperm phylogeny: 17 genes, 640 taxa. American Journal of Botany. 98: 704-30. PMID 21613169 DOI: 10.3732/Ajb.1000404  1
2011 Smith SA, Beaulieu JM, Stamatakis A, Donoghue MJ. Understanding angiosperm diversification using small and large phylogenetic trees. American Journal of Botany. 98: 404-14. PMID 21613134 DOI: 10.3732/Ajb.1000481  1
2010 Goldberg EE, Kohn JR, Lande R, Robertson KA, Smith SA, Igi? B. Species selection maintains self-incompatibility. Science (New York, N.Y.). 330: 493-5. PMID 20966249 DOI: 10.1126/Science.1194513  1
2010 Bendiksby M, Schumacher T, Gussarova G, Nais J, Mat-Salleh K, Sofiyanti N, Madulid D, Smith SA, Barkman T. Elucidating the evolutionary history of the Southeast Asian, holoparasitic, giant-flowered Rafflesiaceae: pliocene vicariance, morphological convergence and character displacement. Molecular Phylogenetics and Evolution. 57: 620-33. PMID 20723606 DOI: 10.1016/J.Ympev.2010.08.005  1
2010 Smith SA, Donoghue MJ. Combining historical biogeography with niche modeling in the Caprifolium clade of Lonicera (Caprifoliaceae, Dipsacales). Systematic Biology. 59: 322-41. PMID 20525639 DOI: 10.1093/Sysbio/Syq011  1
2010 Edwards EJ, Osborne CP, Strömberg CA, Smith SA, Bond WJ, Christin PA, Cousins AB, Duvall MR, Fox DL, Freckleton RP, Ghannoum O, Hartwell J, Huang Y, Janis CM, et al. The origins of C4 grasslands: integrating evolutionary and ecosystem science. Science (New York, N.Y.). 328: 587-91. PMID 20431008 DOI: 10.1126/Science.1177216  1
2010 Smith SA, Beaulieu JM, Donoghue MJ. An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proceedings of the National Academy of Sciences of the United States of America. 107: 5897-902. PMID 20304790 DOI: 10.1073/Pnas.1001225107  1
2010 Edwards EJ, Smith SA. Phylogenetic analyses reveal the shady history of C4 grasses. Proceedings of the National Academy of Sciences of the United States of America. 107: 2532-7. PMID 20142480 DOI: 10.1073/Pnas.0909672107  1
2009 Smith SA, O'Meara BC. Morphogenera, monophyly, and macroevolution. Proceedings of the National Academy of Sciences of the United States of America. 106: E97-8; author reply . PMID 19805242 DOI: 10.1073/Pnas.0906918106  1
2009 Smith SA, Beaulieu JM. Life history influences rates of climatic niche evolution in flowering plants. Proceedings. Biological Sciences / the Royal Society. 276: 4345-52. PMID 19776076 DOI: 10.1098/Rspb.2009.1176  1
2009 Smith SA, Beaulieu JM, Donoghue MJ. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. Bmc Evolutionary Biology. 9: 37. PMID 19210768 DOI: 10.1186/1471-2148-9-37  1
2009 Evans ME, Smith SA, Flynn RS, Donoghue MJ. Climate, niche evolution, and diversification of the "bird-cage" evening primroses (Oenothera, sections Anogra and Kleinia). The American Naturalist. 173: 225-40. PMID 19072708 DOI: 10.1086/595757  1
2009 Smith SA. Taking into account phylogenetic and divergence-time uncertainty in a parametric biogeographical analysis of the Northern Hemisphere plant clade Caprifolieae Journal of Biogeography. 36: 2324-2337. DOI: 10.1111/J.1365-2699.2009.02160.X  1
2009 Cellinese N, Smith SA, Edwards EJ, Kim ST, Haberle RC, Avramakis M, Donoghue MJ. Historical biogeography of the endemic Campanulaceae of Crete Journal of Biogeography. 36: 1253-1269. DOI: 10.1111/J.1365-2699.2008.02077.X  1
2008 Smith SA, Donoghue MJ. Rates of molecular evolution are linked to life history in flowering plants. Science (New York, N.Y.). 322: 86-9. PMID 18832643 DOI: 10.1126/Science.1163197  1
2008 Smith SA, Tank DC, Boulanger LA, Bascom-Slack CA, Eisenman K, Kingery D, Babbs B, Fenn K, Greene JS, Hann BD, Keehner J, Kelley-Swift EG, Kembaiyan V, Lee SJ, Li P, et al. Bioactive endophytes warrant intensified exploration and conservation. Plos One. 3: e3052. PMID 18725962 DOI: 10.1371/Journal.Pone.0003052  1
2008 Dunn CW, Hejnol A, Matus DQ, Pang K, Browne WE, Smith SA, Seaver E, Rouse GW, Obst M, Edgecombe GD, Sørensen MV, Haddock SH, Schmidt-Rhaesa A, Okusu A, Kristensen RM, et al. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature. 452: 745-9. PMID 18322464 DOI: 10.1038/Nature06614  1
2008 Ree RH, Smith SA. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and cladogenesis. Systematic Biology. 57: 4-14. PMID 18253896 DOI: 10.1080/10635150701883881  1
2008 Smith SA, Dunn CW. Phyutility: a phyloinformatics tool for trees, alignments and molecular data. Bioinformatics (Oxford, England). 24: 715-6. PMID 18227120 DOI: 10.1093/Bioinformatics/Btm619  1
2007 Roulston TH, Smith SA, Brewster AL. Short communication: A comparison of pan trap and intensive net sampling techniques for documenting a bee (Hymenoptera: Apiformes) fauna Journal of the Kansas Entomological Society. 80: 179-181. DOI: 10.2317/0022-8567(2007)80[179:Acopta]2.0.Co;2  1
2006 Moore BR, Smith SA, Donoghue MJ. Increasing data transparency and estimating phylogenetic uncertainty in supertrees: Approaches using nonparametric bootstrapping. Systematic Biology. 55: 662-76. PMID 16969942 DOI: 10.1080/10635150600920693  1
2004 Donoghue MJ, Smith SA. Patterns in the assembly of temperate forests around the Northern Hemisphere. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 359: 1633-44. PMID 15519978 DOI: 10.1098/Rstb.2004.1538  1
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