Works by Michael, Todd P.

Results: 63

A Morning-Specific Phytohormone Gene Expression Program underlying Rhythmic Plant Growth.

Published in:

PLoS Biology, 2008, v. 6, n. 9, p. e225, doi. 10.1371/journal.pbio.0060225

By:

Michael, Todd P.;
Breton, Ghislain;
Hazen, Samuel P.;
Priest, Henry;
Mockler, Todd C.;
Kay, Steve A.;
Chory, Joanne

Publication type:

Article

Large structural variations in the haplotype‐resolved African cassava genome.

Published in:

Plant Journal, 2021, v. 108, n. 6, p. 1830, doi. 10.1111/tpj.15543

By:

Mansfeld, Ben N.;
Boyher, Adam;
Berry, Jeffrey C.;
Wilson, Mark;
Ou, Shujun;
Polydore, Seth;
Michael, Todd P.;
Fahlgren, Noah;
Bart, Rebecca S.

Publication type:

Article

Generating a high‐confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies.

Published in:

Plant Journal, 2018, v. 96, n. 3, p. 670, doi. 10.1111/tpj.14049

By:

Hoang, Phuong N.T.;
Michael, Todd P.;
Gilbert, Sarah;
Chu, Philomena;
Motley, S. Timothy;
Appenroth, Klaus J.;
Schubert, Ingo;
Lam, Eric

Publication type:

Article

Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies.

Published in:

Plant Journal, 2017, v. 89, n. 3, p. 617, doi. 10.1111/tpj.13400

By:

Michael, Todd P.;
Bryant, Douglas;
Gutierrez, Ryan;
Borisjuk, Nikolai;
Chu, Philomena;
Zhang, Hanzhong;
Xia, Jing;
Zhou, Junfei;
Peng, Hai;
El Baidouri, Moaine;
Hallers, Boudewijn;
Hastie, Alex R.;
Liang, Tiffany;
Acosta, Kenneth;
Gilbert, Sarah;
McEntee, Connor;
Jackson, Scott A.;
Mockler, Todd C.;
Zhang, Weixiong;
Lam, Eric

Publication type:

Article

The genome of black raspberry ( Rubus occidentalis).

Published in:

Plant Journal, 2016, v. 87, n. 6, p. 535, doi. 10.1111/tpj.13215

By:

VanBuren, Robert;
Bryant, Doug;
Bushakra, Jill M.;
Vining, Kelly J.;
Edger, Patrick P.;
Rowley, Erik R.;
Priest, Henry D.;
Michael, Todd P.;
Lyons, Eric;
Filichkin, Sergei A.;
Dossett, Michael;
Finn, Chad E.;
Bassil, Nahla V.;
Mockler, Todd C.

Publication type:

Article

Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53157-w

By:

Kitony, Justine K.;
Colt, Kelly;
Abramson, Bradley W.;
Hartwick, Nolan T.;
Petrus, Semar;
Konozy, Emadeldin H. E.;
Karimi, Nisa;
Yant, Levi;
Michael, Todd P.

Publication type:

Article

Chromosome-level baobab genome illuminates its evolutionary trajectory and environmental adaptation.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-53157-w

By:

Kitony, Justine K.;
Colt, Kelly;
Abramson, Bradley W.;
Hartwick, Nolan T.;
Petrus, Semar;
Konozy, Emadeldin H. E.;
Karimi, Nisa;
Yant, Levi;
Michael, Todd P.

Publication type:

Article

The carnivorous bladderwort (Utricularia, Lentibulariaceae): a system inflates.

Published in:

Journal of Experimental Botany, 2010, v. 61, n. 1, p. 5, doi. 10.1093/jxb/erp349

By:

Albert, Victor A.;
Jobson, Richard W.;
Michael, Todd P.;
Taylor, Derek J.

Publication type:

Article

Plant genome size variation: bloating and purging DNA.

Published in:

Briefings in Functional Genomics, 2014, v. 13, n. 4, p. 308, doi. 10.1093/bfgp/elu005

By:

Michael, Todd P.

Publication type:

Article

Gapless assembly of maize chromosomes using long-read technologies.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02029-9

By:

Liu, Jianing;
Seetharam, Arun S.;
Chougule, Kapeel;
Ou, Shujun;
Swentowsky, Kyle W.;
Gent, Jonathan I.;
Llaca, Victor;
Woodhouse, Margaret R.;
Manchanda, Nancy;
Presting, Gernot G.;
Kudrna, David A.;
Alabady, Magdy;
Hirsch, Candice N.;
Fengler, Kevin A.;
Ware, Doreen;
Michael, Todd P.;
Hufford, Matthew B.;
Dawe, R. Kelly

Publication type:

Article

Contrasting a reference cranberry genome to a crop wild relative provides insights into adaptation, domestication, and breeding.

Published in:

PLoS ONE, 2022, v. 17, n. 3, p. 1, doi. 10.1371/journal.pone.0264966

By:

Kawash, Joseph;
Colt, Kelly;
Hartwick, Nolan T.;
Abramson, Bradley W.;
Vorsa, Nicholi;
Polashock, James J.;
Michael, Todd P.

Publication type:

Article

Time of day and network reprogramming during drought induced CAM photosynthesis in Sedum album.

Published in:

PLoS Genetics, 2019, v. 15, n. 6, p. 1, doi. 10.1371/journal.pgen.1008209

By:

Wai, Ching Man;
Weise, Sean E.;
Ozersky, Philip;
Mockler, Todd C.;
Michael, Todd P.;
VanBuren, Robert

Publication type:

Article

The complex architecture and epigenomic impact of plant T-DNA insertions.

Published in:

PLoS Genetics, 2019, v. 15, n. 1, p. 1, doi. 10.1371/journal.pgen.1007819

By:

Jupe, Florian;
Rivkin, Angeline C.;
Sandoval, Justin P.;
Chen, Huaming;
Castanon, Rosa;
Nery, Joseph R.;
Zander, Mark;
Ecker, Joseph R.;
Michael, Todd P.;
Motley, S. Timothy;
Slotkin, R. Keith

Publication type:

Article

Scalable Biosynthesis of the Seaweed Neurochemical, Kainic Acid.

Published in:

Angewandte Chemie, 2019, v. 131, n. 25, p. 8542, doi. 10.1002/ange.201902910

By:

Chekan, Jonathan R.;
McKinnie, Shaun M. K.;
Moore, Malia L.;
Poplawski, Shane G.;
Michael, Todd P.;
Moore, Bradley S.

Publication type:

Article

PanKmer: k-mer-based and reference-free pangenome analysis.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad621

By:

Aylward, Anthony J;
Petrus, Semar;
Mamerto, Allen;
Hartwick, Nolan T;
Michael, Todd P

Publication type:

Article

Can a plant biologist fix a thermostat?

Published in:

New Phytologist, 2025, v. 245, n. 4, p. 1403, doi. 10.1111/nph.20382

By:

Michael, Todd P.

Publication type:

Article

Genomics of turions from the Greater Duckweed reveal its pathways for dormancy and re‐emergence strategy.

Published in:

New Phytologist, 2023, v. 239, n. 1, p. 116, doi. 10.1111/nph.18941

By:

Pasaribu, Buntora;
Acosta, Kenneth;
Aylward, Anthony;
Liang, Yuanxue;
Abramson, Bradley W.;
Colt, Kelly;
Hartwick, Nolan T.;
Shanklin, John;
Michael, Todd P.;
Lam, Eric

Publication type:

Article

Characterization of defense responses against bacterial pathogens in duckweeds lacking EDS1.

Published in:

New Phytologist, 2022, v. 236, n. 5, p. 1838, doi. 10.1111/nph.18453

By:

Baggs, Erin L.;
Tiersma, Meije B.;
Abramson, Brad W.;
Michael, Todd P.;
Krasileva, Ksenia V.

Publication type:

Article

A new Cannabis genome assembly associates elevated cannabidiol (CBD) with hemp introgressed into marijuana.

Published in:

New Phytologist, 2021, v. 230, n. 4, p. 1665, doi. 10.1111/nph.17243

By:

Grassa, Christopher J.;
Weiblen, George D.;
Wenger, Jonathan P.;
Dabney, Clemon;
Poplawski, Shane G.;
Timothy Motley, S.;
Michael, Todd P.;
Schwartz, C. J.

Publication type:

Article

Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation.

Published in:

New Phytologist, 2020, v. 227, n. 6, p. 1709, doi. 10.1111/nph.16507

By:

MacKinnon, Kirk J‐M.;
Cole, Benjamin J.;
Yu, Chang;
Coomey, Joshua H.;
Hartwick, Nolan T.;
Remigereau, Marie‐Stanislas;
Duffy, Tomás;
Michael, Todd P.;
Kay, Steve A.;
Hazen, Samuel P.

Publication type:

Article

Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat.

Published in:

New Phytologist, 2019, v. 222, n. 2, p. 1061, doi. 10.1111/nph.15650

By:

Mower, Jeffrey P.;
Ma, Peng‐Fei;
Grewe, Felix;
Taylor, Alex;
Michael, Todd P.;
VanBuren, Robert;
Qiu, Yin‐Long

Publication type:

Article

Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production.

Published in:

Plant Journal, 2013, v. 73, n. 1, p. 77, doi. 10.1111/tpj.12017

By:

Luo, Chongyuan;
Sidote, David J.;
Zhang, Yi;
Kerstetter, Randall A.;
Michael, Todd P.;
Lam, Eric

Publication type:

Article

Retraction Note: Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31001-3

By:

Zhang, Tao;
Mudgett, Michael;
Rambabu, Ratnala;
Abramson, Bradley;
Dai, Xinhua;
Michael, Todd P.;
Zhao, Yunde

Publication type:

Article

Retraction Note: Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis.

Published in:

Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-31001-3

By:

Zhang, Tao;
Mudgett, Michael;
Rambabu, Ratnala;
Abramson, Bradley;
Dai, Xinhua;
Michael, Todd P.;
Zhao, Yunde

Publication type:

Article

Underwater CAM photosynthesis elucidated by Isoetes genome.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26644-7

By:

Wickell, David;
Kuo, Li-Yaung;
Yang, Hsiao-Pei;
Dhabalia Ashok, Amra;
Irisarri, Iker;
Dadras, Armin;
de Vries, Sophie;
de Vries, Jan;
Huang, Yao-Moan;
Li, Zheng;
Barker, Michael S.;
Hartwick, Nolan T.;
Michael, Todd P.;
Li, Fay-Wei

Publication type:

Article

Selective inheritance of target genes from only one parent of sexually reproduced F1 progeny in Arabidopsis.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-24195-5

By:

Zhang, Tao;
Mudgett, Michael;
Rambabu, Ratnala;
Abramson, Bradley;
Dai, Xinhua;
Michael, Todd P.;
Zhao, Yunde

Publication type:

Article

The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana.

Published in:

Nature Genetics, 2006, v. 38, n. 6, p. 711, doi. 10.1038/ng1818

By:

Balasubramanian, Sureshkumar;
Sureshkumar, Sridevi;
Agrawal, Mitesh;
Michael, Todd P.;
Wessinger, Carrie;
Maloof, Julin N.;
Clark, Richard;
Warthmann, Norman;
Chory, Joanne;
Weigel, Detlef

Publication type:

Article

Network Discovery Pipeline Elucidates Conserved Time-of-Day-Specific cis-Regulatory Modules.

Published in:

PLoS Genetics, 2008, v. 4, n. 2, p. 1, doi. 10.1371/journal.pgen.0040014

By:

Michael, Todd P.;
Mockler, Todd C.;
Breton, Ghislain;
McEntee^1, Connor;
Byer^1, Amanda;
Trout, Jonathan D.;
Hazen, Samuel P.;
Rongkun Shen;
Priest, Henry D.;
Sullivan, Christopher M.;
Givan, Scott A.;
Yanovsky, Marcelo;
Fangxin Hong;
Kay, Steve A.;
Chory, Joanne

Publication type:

Article

Crossing the Pacific: Genomics Reveals the Presence of Japanese Sardine (Sardinops melanosticta) in the California Current Large Marine Ecosystem.

Published in:

Molecular Ecology, 2024, v. 33, n. 22, p. 1, doi. 10.1111/mec.17561

By:

Longo, Gary C.;
Minich, Jeremiah J.;
Allsing, Nicholas;
James, Kelsey;
Adams‐Herrmann, Ella S.;
Larson, Wes;
Hartwick, Nolan;
Duong, Tiffany;
Muhling, Barbara;
Michael, Todd P.;
Craig, Matthew T.

Publication type:

Article

The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza.

Published in:

G3: Genes | Genomes | Genetics, 2024, v. 14, n. 4, p. 1, doi. 10.1093/g3journal/jkae004

By:

Harkess, Alex;
Bewick, Adam J;
Lu, Zefu;
Fourounjian, Paul;
Michael, Todd P;
Schmitz, Robert J;
Meyers, Blake C

Publication type:

Article

Improved Spirodela polyrhiza genome and proteomic analyses reveal a conserved chromosomal structure with high abundance of chloroplastic proteins favoring energy production.

Published in:

Journal of Experimental Botany, 2021, v. 72, n. 7, p. 2491, doi. 10.1093/jxb/erab006

By:

Harkess, Alex;
McLoughlin, Fionn;
Bilkey, Natasha;
Elliott, Kiona;
Emenecker, Ryan;
Mattoon, Erin;
Miller, Kari;
Czymmek, Kirk;
Vierstra, Richard D;
Meyers, Blake C;
Michael, Todd P

Publication type:

Article

The Chloroplast Genome of Utricularia reniformis Sheds Light on the Evolution of the ndh Gene Complex of Terrestrial Carnivorous Plants from the Lentibulariaceae Family.

Published in:

PLoS ONE, 2016, v. 11, n. 10, p. 1, doi. 10.1371/journal.pone.0165176

By:

Silva, Saura R.;
Diaz, Yani C. A.;
Penha, Helen Alves;
Pinheiro, Daniel G.;
Fernandes, Camila C.;
Miranda, Vitor F. O.;
Michael, Todd P.;
Varani, Alessandro M.

Publication type:

Article

Gross Chromosomal Rearrangements in Kluyveromyces marxianus Revealed by Illumina and Oxford Nanopore Sequencing.

Published in:

International Journal of Molecular Sciences, 2020, v. 21, n. 19, p. 7112, doi. 10.3390/ijms21197112

By:

Ding, Lin;
Macdonald, Harrison D.;
Smith, Hamilton O.;
Hutchison III, Clyde A.;
Merryman, Chuck;
Michael, Todd P.;
Abramson, Bradley W.;
Kannan, Krishna;
Liang, Joe;
Gill, John;
Gibson, Daniel G.;
Glass, John I.

Publication type:

Article

The Terrestrial Carnivorous Plant Utricularia reniformis Sheds Light on Environmental and Life-Form Genome Plasticity.

Published in:

International Journal of Molecular Sciences, 2020, v. 21, n. 1, p. 3, doi. 10.3390/ijms21010003

By:

Silva, Saura R.;
Moraes, Ana Paula;
Penha, Helen A.;
Julião, Maria H. M.;
Domingues, Douglas S.;
Michael, Todd P.;
Miranda, Vitor F. O.;
Varani, Alessandro M.

Publication type:

Article

Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes.

Published in:

International Journal of Molecular Sciences, 2019, v. 20, n. 24, p. 6130, doi. 10.3390/ijms20246130

By:

Silva, Saura R.;
Pinheiro, Daniel G.;
Penha, Helen A.;
Płachno, Bartosz J.;
Michael, Todd P.;
Meer, Elliott J.;
Miranda, Vitor F. O.;
Varani, Alessandro M.

Publication type:

Article

Return of the Lemnaceae: duckweed as a model plant system in the genomics and postgenomics era.

Published in:

Plant Cell, 2021, v. 33, n. 10, p. 3207, doi. 10.1093/plcell/koab189

By:

Acosta, Kenneth;
Appenroth, Klaus J;
Borisjuk, Ljudmilla;
Edelman, Marvin;
Heinig, Uwe;
Jansen, Marcel A K;
Oyama, Tokitaka;
Pasaribu, Buntora;
Schubert, Ingo;
Sorrels, Shawn;
Sree, K Sowjanya;
Xu, Shuqing;
Michael, Todd P;
Lam, Eric

Publication type:

Article

Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption.

Published in:

PLoS ONE, 2018, v. 13, n. 2, p. 1, doi. 10.1371/journal.pone.0192772

By:

Minich, Jeremiah J.;
Morris, Megan M.;
Brown, Matt;
Doane, Michael;
Edwards, Matthew S.;
Michael, Todd P.;
Dinsdale, Elizabeth A.

Publication type:

Article

Comparative genomic analysis of Genlisea (corkscrew plants—Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes.

Published in:

PLoS ONE, 2018, v. 13, n. 1, p. 1, doi. 10.1371/journal.pone.0190321

By:

Silva, Saura R.;
Michael, Todd P.;
Meer, Elliott J.;
Pinheiro, Daniel G.;
Varani, Alessandro M.;
Miranda, Vitor F. O.

Publication type:

Article

The mitochondrial genome of the terrestrial carnivorous plant Utricularia reniformis (Lentibulariaceae): Structure, comparative analysis and evolutionary landmarks.

Published in:

PLoS ONE, 2017, v. 12, n. 7, p. 1, doi. 10.1371/journal.pone.0180484

By:

Silva, Saura R.;
Alvarenga, Danillo O.;
Aranguren, Yani;
Penha, Helen A.;
Fernandes, Camila C.;
Pinheiro, Daniel G.;
Oliveira, Marcos T.;
Michael, Todd P.;
Miranda, Vitor F. O.;
Varani, Alessandro M.

Publication type:

Article

Scalable Biosynthesis of the Seaweed Neurochemical, Kainic Acid.

Published in:

Angewandte Chemie International Edition, 2019, v. 58, n. 25, p. 8454, doi. 10.1002/anie.201902910

By:

Chekan, Jonathan R.;
McKinnie, Shaun M. K.;
Moore, Malia L.;
Poplawski, Shane G.;
Michael, Todd P.;
Moore, Bradley S.

Publication type:

Article

Filtering error from SOLiD Output.

Published in:

Bioinformatics, 2010, v. 26, n. 6, p. 849, doi. 10.1093/bioinformatics/btq045

By:

Sasson, Ariella;
Michael, Todd P.

Publication type:

Article

The seed transcriptome of Rafflesia reveals horizontal gene transfer and convergent evolution: Implications for conserving the world's largest flower.

Published in:

Plants, People, Planet, 2025, v. 7, n. 2, p. 448, doi. 10.1002/ppp3.10370

By:

Molina, Jeanmaire;
Wicaksono, Adhityo;
Michael, Todd P.;
Kwak, Su‐Hwan;
Pedales, Ronniel D.;
Joly‐Lopez, Zoé;
Petrus, Semar;
Mamerto, Allen;
Tomek, Brian;
Ahmed, Sumaya;
Maddu, Venkatasivasankar;
Yakubova, Kristina;
Tandang, Danilo;
Morin, Joseph W.;
Park, So‐Yon;
Lee, Hyun‐Oh;
McLaughlin, William;
Wallick, Kyle;
Adams, James;
Novy, Ari

Publication type:

Article

Optimization of Molecular Methods for Detecting Duckweed-Associated Bacteria.

Published in:

Plants (2223-7747), 2023, v. 12, n. 4, p. 872, doi. 10.3390/plants12040872

By:

Acosta, Kenneth;
Sorrels, Shawn;
Chrisler, William;
Huang, Weijuan;
Gilbert, Sarah;
Brinkman, Thomas;
Michael, Todd P.;
Lebeis, Sarah L.;
Lam, Eric

Publication type:

Article

Allopolyploid origin and diversification of the Hawaiian endemic mints.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-47247-y

By:

Tomlin, Crystal M.;
Rajaraman, Sitaram;
Sebesta, Jeanne Theresa;
Scheen, Anne-Cathrine;
Bendiksby, Mika;
Low, Yee Wen;
Salojärvi, Jarkko;
Michael, Todd P.;
Albert, Victor A.;
Lindqvist, Charlotte

Publication type:

Article

A review of using duckweed (Lemnaceae) in fish feeds.

Published in:

Reviews in Aquaculture, 2024, v. 16, n. 3, p. 1212, doi. 10.1111/raq.12892

By:

Minich, Jeremiah J.;
Michael, Todd P.

Publication type:

Article

Time of Day Analysis over a Field Grown Developmental Time Course in Rice.

Published in:

Plants (2223-7747), 2023, v. 12, n. 1, p. 166, doi. 10.3390/plants12010166

By:

Michael, Todd P.

Publication type:

Article

Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms.

Published in:

Annals of Botany, 2014, v. 114, n. 8, p. 1651, doi. 10.1093/aob/mcu189

By:

Fleischmann, Andreas;
Sousa, Aretuza;
Heubl, Günther;
Michael, Todd P.;
Wang, Wenqin;
Rivadavia, Fernando;
Temsch, Eva M.;
Greilhuber, Johann;
Müller, Kai F.

Publication type:

Article

Assembly of Mitochondrial Genomes Using Nanopore Long‐Read Technology in Three Sea Chubs (Teleostei: Kyphosidae).

Published in:

Molecular Ecology Resources, 2025, v. 25, n. 1, p. 1, doi. 10.1111/1755-0998.14034

By:

Baeza, J. Antonio;
Minish, Jeremiah J.;
Michael, Todd P.

Publication type:

Article

Core circadian clock and light signaling genes brought into genetic linkage across the green lineage.

Published in:

Plant Physiology, 2022, v. 190, n. 2, p. 1037, doi. 10.1093/plphys/kiac276

By:

Michael, Todd P.

Publication type:

Article

SOPRA: Scaffolding algorithm for paired reads viastatistical optimization.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 345, doi. 10.1186/1471-2105-11-345

By:

Dayarian, Adel;
Michael, Todd P.;
Sengupta, Anirvan M.

Publication type:

Article