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Sequencing and Analyzing the Transcriptomes of a Thousand Species Across the Tree of Life for Green Plants.

Wong GK, Soltis DE, Leebens-Mack J, Wickett NJ, Barker MS, Van de Peer Y, Graham SW, Melkonian M.

Annu Rev Plant Biol. 2019 Dec 18. doi: 10.1146/annurev-arplant-042916-041040. [Epub ahead of print]


Genomes of early-diverging streptophyte algae shed light on plant terrestrialization.

Wang S, Li L, Li H, Sahu SK, Wang H, Xu Y, Xian W, Song B, Liang H, Cheng S, Chang Y, Song Y, Çebi Z, Wittek S, Reder T, Peterson M, Yang H, Wang J, Melkonian B, Van de Peer Y, Xu X, Wong GK, Melkonian M, Liu H, Liu X.

Nat Plants. 2019 Dec 16. doi: 10.1038/s41477-019-0560-3. [Epub ahead of print]


The Draft Genome of the Small, Spineless Green Alga Desmodesmus costato-granulatus (Sphaeropleales, Chlorophyta).

Wang S, Li L, Xu Y, Melkonian B, Lorenz M, Friedl T, Petersen M, Sahu SK, Melkonian M, Liu H.

Protist. 2019 Dec;170(6):125697. doi: 10.1016/j.protis.2019.125697. Epub 2019 Oct 25.


The Draft Genome of Hariotina reticulata (Sphaeropleales, Chlorophyta) Provides Insight into the Evolution of Scenedesmaceae.

Xu Y, Li L, Liang H, Melkonian B, Lorenz M, Friedl T, Petersen M, Liu H, Melkonian M, Wang S.

Protist. 2019 Dec;170(6):125684. doi: 10.1016/j.protis.2019.125684. Epub 2019 Oct 19.


Genomes of Subaerial Zygnematophyceae Provide Insights into Land Plant Evolution.

Cheng S, Xian W, Fu Y, Marin B, Keller J, Wu T, Sun W, Li X, Xu Y, Zhang Y, Wittek S, Reder T, Günther G, Gontcharov A, Wang S, Li L, Liu X, Wang J, Yang H, Xu X, Delaux PM, Melkonian B, Wong GK, Melkonian M.

Cell. 2019 Nov 14;179(5):1057-1067.e14. doi: 10.1016/j.cell.2019.10.019.


Biomass and Astaxanthin Productivities of Haematococcus pluvialis in an Angled Twin-Layer Porous Substrate Photobioreactor: Effect of Inoculum Density and Storage Time.

Do TT, Ong BN, Nguyen Tran ML, Nguyen D, Melkonian M, Tran HD.

Biology (Basel). 2019 Sep 18;8(3). pii: E68. doi: 10.3390/biology8030068.


Molecular evidence for origin, diversification and ancient gene duplication of plant subtilases (SBTs).

Xu Y, Wang S, Li L, Sahu SK, Petersen M, Liu X, Melkonian M, Zhang G, Liu H.

Sci Rep. 2019 Aug 28;9(1):12485. doi: 10.1038/s41598-019-48664-6.


Gains and losses of metabolic function inferred from a phylotranscriptomic analysis of algae.

Goh FQY, Jeyakani J, Tipthara P, Cazenave-Gassiot A, Ghosh R, Bogard N, Yeo Z, Wong GK, Melkonian M, Wenk MR, Clarke ND.

Sci Rep. 2019 Jul 19;9(1):10482. doi: 10.1038/s41598-019-46869-3.


Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida.

Liang H, Wei T, Xu Y, Li L, Kumar Sahu S, Wang H, Li H, Fu X, Zhang G, Melkonian M, Liu X, Wang S, Liu H.

Int J Mol Sci. 2019 Jun 20;20(12). pii: E3020. doi: 10.3390/ijms20123020.


Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land.

Zhao C, Wang Y, Chan KX, Marchant DB, Franks PJ, Randall D, Tee EE, Chen G, Ramesh S, Phua SY, Zhang B, Hills A, Dai F, Xue D, Gilliham M, Tyerman S, Nevo E, Wu F, Zhang G, Wong GK, Leebens-Mack JH, Melkonian M, Blatt MR, Soltis PS, Soltis DE, Pogson BJ, Chen ZH.

Proc Natl Acad Sci U S A. 2019 Mar 12;116(11):5015-5020. doi: 10.1073/pnas.1812092116. Epub 2019 Feb 25.


Extending the Time Domain of Neuronal Silencing with Cryptophyte Anion Channelrhodopsins.

Govorunova EG, Sineshchekov OA, Hemmati R, Janz R, Morelle O, Melkonian M, Wong GK, Spudich JL.

eNeuro. 2018 Jul 10;5(3). pii: ENEURO.0174-18.2018. doi: 10.1523/ENEURO.0174-18.2018. eCollection 2018 May-Jun.


10KP: A phylodiverse genome sequencing plan.

Cheng S, Melkonian M, Smith SA, Brockington S, Archibald JM, Delaux PM, Li FW, Melkonian B, Mavrodiev EV, Sun W, Fu Y, Yang H, Soltis DE, Graham SW, Soltis PS, Liu X, Xu X, Wong GK.

Gigascience. 2018 Mar 1;7(3):1-9. doi: 10.1093/gigascience/giy013.


Origin and evolution of the nuclear auxin response system.

Mutte SK, Kato H, Rothfels C, Melkonian M, Wong GK, Weijers D.

Elife. 2018 Mar 27;7. pii: e33399. doi: 10.7554/eLife.33399.


Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis.

Jensen JK, Busse-Wicher M, Poulsen CP, Fangel JU, Smith PJ, Yang JY, Peña MJ, Dinesen MH, Martens HJ, Melkonian M, Wong GK, Moremen KW, Wilkerson CG, Scheller HV, Dupree P, Ulvskov P, Urbanowicz BR, Harholt J.

New Phytol. 2018 May;218(3):1049-1060. doi: 10.1111/nph.15050. Epub 2018 Feb 20.


A Re-investigation of Sarcinochrysis marina (Sarcinochrysidales, Pelagophyceae) from its Type Locality and the Descriptions of Arachnochrysis, Pelagospilus, Sargassococcus and Sungminbooa genera nov.

Han KY, Graf L, Reyes CP, Melkonian B, Andersen RA, Yoon HS, Melkonian M.

Protist. 2018 Feb;169(1):79-106. doi: 10.1016/j.protis.2017.12.004. Epub 2018 Jan 11.


Molecular phylogeny, systematics, and revision of the type species of Lobomonas, L. francei (Volvocales, Chlorophyta) and closely related taxa.

Sausen N, Malavasi V, Melkonian M.

J Phycol. 2018 Apr;54(2):198-214. doi: 10.1111/jpy.12615. Epub 2018 Jan 30.


Biofilm-based photobioreactors: their design and improving productivity through efficient supply of dissolved inorganic carbon.

Li T, Strous M, Melkonian M.

FEMS Microbiol Lett. 2017 Dec 29;364(24). doi: 10.1093/femsle/fnx218. Review.


Growth and biomass productivity of Scenedesmus vacuolatus on a twin layer system and a comparison with other types of cultivations.

Carbone DA, Olivieri G, Pollio A, Gabriele, Melkonian M.

Appl Microbiol Biotechnol. 2017 Dec;101(23-24):8321-8329. doi: 10.1007/s00253-017-8515-y. Epub 2017 Oct 14.


Corrigendum to "Revision of the Genus Cryptomonas (Cryptophyceae): A Combination of Molecular Phylogeny and Morphology Provides Insights into a Long-Hidden Dimorphism" [Protist 154 (2003) 371-409].

Hoef-Emden K, Melkonian M.

Protist. 2017 Aug;168(4):467. doi: 10.1016/j.protis.2017.06.003. Epub 2017 Aug 17. No abstract available.


Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

Johnson KL, Cassin AM, Lonsdale A, Wong GK, Soltis DE, Miles NW, Melkonian M, Melkonian B, Deyholos MK, Leebens-Mack J, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Carpenter EJ, Bacic A, Doblin MS, Schultz CJ.

Plant Physiol. 2017 Jun;174(2):904-921. doi: 10.1104/pp.17.00295. Epub 2017 Apr 26.


Bleeding risk of antiplatelet drugs compared with oral anticoagulants in older patients with atrial fibrillation: a systematic review and meta-analysis.

Melkonian M, Jarzebowski W, Pautas E, Siguret V, Belmin J, Lafuente-Lafuente C.

J Thromb Haemost. 2017 Jul;15(7):1500-1510. doi: 10.1111/jth.13697. Epub 2017 May 11. Review.


The Expanding Family of Natural Anion Channelrhodopsins Reveals Large Variations in Kinetics, Conductance, and Spectral Sensitivity.

Govorunova EG, Sineshchekov OA, Rodarte EM, Janz R, Morelle O, Melkonian M, Wong GK, Spudich JL.

Sci Rep. 2017 Mar 3;7:43358. doi: 10.1038/srep43358.


Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora.

Nowack EC, Price DC, Bhattacharya D, Singer A, Melkonian M, Grossman AR.

Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12214-12219. Epub 2016 Oct 10.


The Evolution of HD2 Proteins in Green Plants.

Bourque S, Jeandroz S, Grandperret V, Lehotai N, Aimé S, Soltis DE, Miles NW, Melkonian M, Deyholos MK, Leebens-Mack JH, Chase MW, Rothfels CJ, Stevenson DW, Graham SW, Wang X, Wu S, Pires JC, Edger PP, Yan Z, Xie Y, Carpenter EJ, Wong GKS, Wendehenne D, Nicolas-Francès V.

Trends Plant Sci. 2016 Dec;21(12):1008-1016. doi: 10.1016/j.tplants.2016.10.001. Epub 2016 Oct 24. Review.


Obituary: Eberhard Schnepf (April 4, 1931-April 10, 2016).

Bothe H, Melkonian M.

Protist. 2016 Nov;167(5):460-463. doi: 10.1016/j.protis.2016.08.004. Epub 2016 Aug 29. No abstract available.


Porous Substrate Bioreactors: A Paradigm Shift in Microalgal Biotechnology?

Podola B, Li T, Melkonian M.

Trends Biotechnol. 2017 Feb;35(2):121-132. doi: 10.1016/j.tibtech.2016.06.004. Epub 2016 Jul 12. Review.


Apparition of the NAC Transcription Factors Predates the Emergence of Land Plants.

Maugarny-Calès A, Gonçalves B, Jouannic S, Melkonian M, Ka-Shu Wong G, Laufs P.

Mol Plant. 2016 Sep 6;9(9):1345-1348. doi: 10.1016/j.molp.2016.05.016. Epub 2016 Jun 11. No abstract available.


Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology.

Lane TS, Rempe CS, Davitt J, Staton ME, Peng Y, Soltis DE, Melkonian M, Deyholos M, Leebens-Mack JH, Chase M, Rothfels CJ, Stevenson D, Graham SW, Yu J, Liu T, Pires JC, Edger PP, Zhang Y, Xie Y, Zhu Y, Carpenter E, Wong GK, Stewart CN Jr.

BMC Biotechnol. 2016 May 31;16(1):47. doi: 10.1186/s12896-016-0277-6.


Genetic Analysis of Physcomitrella patens Identifies ABSCISIC ACID NON-RESPONSIVE, a Regulator of ABA Responses Unique to Basal Land Plants and Required for Desiccation Tolerance.

Stevenson SR, Kamisugi Y, Trinh CH, Schmutz J, Jenkins JW, Grimwood J, Muchero W, Tuskan GA, Rensing SA, Lang D, Reski R, Melkonian M, Rothfels CJ, Li FW, Larsson A, Wong GK, Edwards TA, Cuming AC.

Plant Cell. 2016 Jun;28(6):1310-27. doi: 10.1105/tpc.16.00091. Epub 2016 May 18.


Occurrence, structure, and evolution of nitric oxide synthase-like proteins in the plant kingdom.

Jeandroz S, Wipf D, Stuehr DJ, Lamattina L, Melkonian M, Tian Z, Zhu Y, Carpenter EJ, Wong GK, Wendehenne D.

Sci Signal. 2016 Mar 1;9(417):re2. doi: 10.1126/scisignal.aad4403. Review.


Functional and topological diversity of LOV domain photoreceptors.

Glantz ST, Carpenter EJ, Melkonian M, Gardner KH, Boyden ES, Wong GK, Chow BY.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):E1442-51. doi: 10.1073/pnas.1509428113. Epub 2016 Feb 29.


International note: Prediction of mathematics work ethic and performance from behavioral, normative, and control beliefs among Qatari adolescents.

Areepattamannil S, Abdelfattah F, Mahasneh RA, Khine MS, Welch AG, Melkonian M, Al Nuaimi SA.

J Adolesc. 2016 Jan;46:38-44. doi: 10.1016/j.adolescence.2015.10.016. Epub 2015 Nov 14.


"Candidatus Finniella" (Rickettsiales, Alphaproteobacteria), Novel Endosymbionts of Viridiraptorid Amoeboflagellates (Cercozoa, Rhizaria).

Hess S, Suthaus A, Melkonian M.

Appl Environ Microbiol. 2015 Nov 13;82(2):659-70. doi: 10.1128/AEM.02680-15. Print 2016 Jan 15.


Microscale profiling of photosynthesis-related variables in a highly productive biofilm photobioreactor.

Li T, Piltz B, Podola B, Dron A, de Beer D, Melkonian M.

Biotechnol Bioeng. 2016 May;113(5):1046-55. doi: 10.1002/bit.25867. Epub 2015 Nov 20.


Algal ancestor of land plants was preadapted for symbiosis.

Delaux PM, Radhakrishnan GV, Jayaraman D, Cheema J, Malbreil M, Volkening JD, Sekimoto H, Nishiyama T, Melkonian M, Pokorny L, Rothfels CJ, Sederoff HW, Stevenson DW, Surek B, Zhang Y, Sussman MR, Dunand C, Morris RJ, Roux C, Wong GK, Oldroyd GE, Ané JM.

Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):13390-5. doi: 10.1073/pnas.1515426112. Epub 2015 Oct 5.


Barrancaceae: A new green algal lineage with structural and behavioral adaptations to a fluctuating environment.

Caisová L, Reyes CP, Álamo VC, Quintana AM, Surek B, Melkonian M.

Am J Bot. 2015 Sep;102(9):1482-92. doi: 10.3732/ajb.1500199. Epub 2015 Sep 7.


The origin and evolution of phototropins.

Li FW, Rothfels CJ, Melkonian M, Villarreal JC, Stevenson DW, Graham SW, Wong GK, Mathews S, Pryer KM.

Front Plant Sci. 2015 Aug 12;6:637. doi: 10.3389/fpls.2015.00637. eCollection 2015.


A method to determine photosynthetic activity from oxygen microsensor data in biofilms subjected to evaporation.

Li T, Podola B, de Beer D, Melkonian M.

J Microbiol Methods. 2015 Oct;117:100-7. doi: 10.1016/j.mimet.2015.07.022. Epub 2015 Jul 29.


Phytochrome diversity in green plants and the origin of canonical plant phytochromes.

Li FW, Melkonian M, Rothfels CJ, Villarreal JC, Stevenson DW, Graham SW, Wong GK, Pryer KM, Mathews S.

Nat Commun. 2015 Jul 28;6:7852. doi: 10.1038/ncomms8852.


International note: Are Emirati parents' attitudes toward mathematics linked to their adolescent children's attitudes toward mathematics and mathematics achievement?

Areepattamannil S, Khine MS, Melkonian M, Welch AG, Al Nuaimi SA, Rashad FF.

J Adolesc. 2015 Oct;44:17-20. doi: 10.1016/j.adolescence.2015.07.002. Epub 2015 Jul 16.


The Origin and Evolution of the Plant Cell Surface: Algal Integrin-Associated Proteins and a New Family of Integrin-Like Cytoskeleton-ECM Linker Proteins.

Becker B, Doan JM, Wustman B, Carpenter EJ, Chen L, Zhang Y, Wong GK, Melkonian M.

Genome Biol Evol. 2015 May 14;7(6):1580-9. doi: 10.1093/gbe/evv089.


Psychological trauma and help seeking behaviour amongst resettled Iraqi refugees in attending English tuition classes in Australia.

Slewa-Younan S, Mond JM, Bussion E, Melkonian M, Mohammad Y, Dover H, Smith M, Milosevic D, Jorm AF.

Int J Ment Health Syst. 2015 Jan 20;9:5. doi: 10.1186/1752-4458-9-5. eCollection 2015.


Continuous removal of zinc from wastewater and mine dump leachate by a microalgal biofilm PSBR.

Li T, Lin G, Podola B, Melkonian M.

J Hazard Mater. 2015 Oct 30;297:112-8. doi: 10.1016/j.jhazmat.2015.04.080. Epub 2015 Apr 30.


Protist--continuity and change.

Melkonian M.

Protist. 2015 Feb;166(1):172. doi: 10.1016/j.protis.2015.01.002. Epub 2015 Jan 17. No abstract available.


Evolution. Response to Comment on "A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity".

Brockington SF, Moyroud E, Sayou C, Monniaux M, Nanao MH, Thévenon E, Chahtane H, Warthmann N, Melkonian M, Zhang Y, Wong GK, Weigel D, Dumas R, Parcy F.

Science. 2015 Feb 6;347(6222):621. doi: 10.1126/science.1256011.


Data access for the 1,000 Plants (1KP) project.

Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK.

Gigascience. 2014 Oct 27;3:17. doi: 10.1186/2047-217X-3-17. eCollection 2014. Review.


International note: exploring differences in native and immigrant adolescents' mathematics achievement and dispositions towards mathematics in Qatar.

Areepattamannil S, Melkonian M, Khine MS.

J Adolesc. 2015 Apr;40:11-3. doi: 10.1016/j.adolescence.2014.12.010. Epub 2015 Jan 16.


Phylotranscriptomic analysis of the origin and early diversification of land plants.

Wickett NJ, Mirarab S, Nguyen N, Warnow T, Carpenter E, Matasci N, Ayyampalayam S, Barker MS, Burleigh JG, Gitzendanner MA, Ruhfel BR, Wafula E, Der JP, Graham SW, Mathews S, Melkonian M, Soltis DE, Soltis PS, Miles NW, Rothfels CJ, Pokorny L, Shaw AJ, DeGironimo L, Stevenson DW, Surek B, Villarreal JC, Roure B, Philippe H, dePamphilis CW, Chen T, Deyholos MK, Baucom RS, Kutchan TM, Augustin MM, Wang J, Zhang Y, Tian Z, Yan Z, Wu X, Sun X, Wong GK, Leebens-Mack J.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4859-68. doi: 10.1073/pnas.1323926111. Epub 2014 Oct 29.


Addendum: independent optical excitation of distinct neural populations.

Klapoetke NC, Murata Y, Kim SS, Pulver SR, Birdsey-Benson A, Cho YK, Morimoto TK, Chuong AS, Carpenter EJ, Tian Z, Wang J, Xie Y, Yan Z, Zhang Y, Chow BY, Surek B, Melkonian M, Jayaraman V, Constantine-Paton M, Wong GK, Edward S Boyden ES.

Nat Methods. 2014 Sep;11(9):972. No abstract available.


Ultrastructure of the Algivorous Amoeboflagellate Viridiraptor invadens (Glissomonadida, Cercozoa).

Hess S, Melkonian M.

Protist. 2014 Sep;165(5):605-35. doi: 10.1016/j.protis.2014.07.004. Epub 2014 Jul 21.


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