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Alexandre Marand - Publications

Affiliations: 
University of Michigan, Ann Arbor, Ann Arbor, MI 
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28 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
2024 Zhang X, Marand AP, Yan H, Schmitz RJ. scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. Genome Biology. 25: 90. PMID 38589969 DOI: 10.1186/s13059-024-03235-5  0.671
2024 Yan H, Mendieta JP, Zhang X, Marand AP, Liang Y, Luo Z, Roulé T, Wagner D, Tu X, Wang Y, Zhong S, Wessler SR, Schmitz RJ. Evolution of cell-type-specific accessible chromatin regions and the -regulatory elements that drive lineage-specific innovation. Biorxiv : the Preprint Server For Biology. PMID 38260561 DOI: 10.1101/2024.01.08.574753  0.665
2023 Zhang X, Marand AP, Yan H, Schmitz RJ. Massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. Biorxiv : the Preprint Server For Biology. PMID 37786710 DOI: 10.1101/2023.09.17.558155  0.665
2023 Minow MAA, Marand AP, Schmitz RJ. Leveraging Single-Cell Populations to Uncover the Genetic Basis of Complex Traits. Annual Review of Genetics. PMID 37562412 DOI: 10.1146/annurev-genet-022123-110824  0.626
2022 Marand AP, Eveland AL, Kaufmann K, Springer NM. -Regulatory Elements in Plant Development, Adaptation, and Evolution. Annual Review of Plant Biology. PMID 36608347 DOI: 10.1146/annurev-arplant-070122-030236  0.411
2022 Wrightsman T, Marand AP, Crisp PA, Springer NM, Buckler ES. Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks. The Plant Genome. e20249. PMID 35924336 DOI: 10.1002/tpg2.20249  0.345
2022 Tu X, Marand AP, Schmitz RJ, Zhong S. A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells. Plant Communications. 100308. PMID 35605196 DOI: 10.1016/j.xplc.2022.100308  0.676
2021 Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S. Chromatin accessibility profiling methods. Nature Reviews. Methods Primers. 1. PMID 38410680 DOI: 10.1038/s43586-020-00008-9  0.694
2021 Noshay JM, Liang Z, Zhou P, Crisp PA, Marand AP, Hirsch CN, Schmitz RJ, Springer NM. Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3 (Bethesda, Md.). 11. PMID 34849810 DOI: 10.1093/g3journal/jkab190  0.671
2021 Schmitz RJ, Marand AP, Zhang X, Mosher RA, Turck F, Chen X, Axtell MJ, Zhong X, Brady SM, Megraw M, Meyers BC. Quality control and evaluation of plant epigenomics data. The Plant Cell. PMID 34648025 DOI: 10.1093/plcell/koab255  0.659
2021 Mendieta JP, Marand AP, Ricci WA, Zhang X, Schmitz RJ. Leveraging histone modifications to improve genome annotations. G3 (Bethesda, Md.). 11. PMID 34568920 DOI: 10.1093/g3journal/jkab263  0.674
2021 Marand AP, Zhang X, Nelson J, Braga Dos Reis PA, Schmitz RJ. Profiling single-cell chromatin accessibility in plants. Star Protocols. 2: 100737. PMID 34430912 DOI: 10.1016/j.xpro.2021.100737  0.608
2021 Marand AP, Schmitz RJ. Single-cell analysis of cis-regulatory elements. Current Opinion in Plant Biology. 65: 102094. PMID 34390932 DOI: 10.1016/j.pbi.2021.102094  0.653
2021 Hufford MB, Seetharam AS, Woodhouse MR, Chougule KM, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Della Coletta R, Tittes S, Hudson AI, Marand AP, Wei S, et al. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science (New York, N.Y.). 373: 655-662. PMID 34353948 DOI: 10.1126/science.abg5289  0.664
2021 Marand AP, Chen Z, Gallavotti A, Schmitz RJ. A cis-regulatory atlas in maize at single-cell resolution. Cell. PMID 33964211 DOI: 10.1016/j.cell.2021.04.014  0.688
2021 Noshay JM, Marand AP, Anderson SN, Zhou P, Mejia Guerra MK, Lu Z, O'Connor CH, Crisp PA, Hirsch CN, Schmitz RJ, Springer NM. Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons. Genetics. 217: 1-13. PMID 33683350 DOI: 10.1093/genetics/iyaa003  0.661
2020 Crisp PA, Marand AP, Noshay JM, Zhou P, Lu Z, Schmitz RJ, Springer NM. Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. Proceedings of the National Academy of Sciences of the United States of America. PMID 32879011 DOI: 10.1073/Pnas.2010250117  0.695
2020 Kieft R, Zhang Y, Marand AP, Moran JD, Bridger R, Wells L, Schmitz RJ, Sabatini R. Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes. Plos Genetics. 16: e1008390. PMID 32084124 DOI: 10.1371/Journal.Pgen.1008390  0.505
2020 Ricci WA, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG, Zhai J, Scanlon MJ, et al. Author Correction: Widespread long-range cis-regulatory elements in the maize genome. Nature Plants. PMID 32029893 DOI: 10.1038/S41477-020-0600-Z  0.609
2019 Ricci WA, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG, Zhai J, Scanlon MJ, et al. Widespread long-range cis-regulatory elements in the maize genome. Nature Plants. PMID 31740773 DOI: 10.1038/S41477-019-0547-0  0.662
2019 Lu Z, Marand AP, Ricci WA, Ethridge CL, Zhang X, Schmitz RJ. The prevalence, evolution and chromatin signatures of plant regulatory elements. Nature Plants. PMID 31740772 DOI: 10.1038/S41477-019-0548-Z  0.643
2019 Marand AP, Jansky SH, Gage JL, Hamernik AJ, de Leon N, Jiang J. Residual Heterozygosity and Epistatic Interactions Underlie the Complex Genetic Architecture of Yield in Diploid Potato. Genetics. PMID 30885982 DOI: 10.1534/genetics.119.302036  0.324
2019 Marand AP, Zhao H, Zhang W, Zeng Z, Fang C, Jiang J. Historical Meiotic Crossover Hotspots Fueled Patterns of Evolutionary Divergence in Rice. The Plant Cell. PMID 30705136 DOI: 10.1105/tpc.18.00750  0.373
2018 Zhao H, Zhang W, Chen L, Wang L, Marand AP, Wu Y, Jiang J. Proliferation of regulatory DNA elements derived from transposable elements in the maize genome. Plant Physiology. PMID 29463772 DOI: 10.1104/pp.17.01467  0.516
2018 Leisner CP, Hamilton JP, Crisovan E, Manrique-Carpintero NC, Marand AP, Newton L, Pham GM, Jiang J, Douches DS, Jansky SH, Buell CR. Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity. The Plant Journal : For Cell and Molecular Biology. PMID 29405524 DOI: 10.1111/tpj.13857  0.426
2017 Marand AP, Jansky SH, Zhao H, Leisner CP, Zhu X, Zeng Z, Crisovan E, Newton L, Hamernik AJ, Veilleux RE, Buell CR, Jiang J. Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato. Genome Biology. 18: 203. PMID 29084572 DOI: 10.1186/S13059-017-1326-8  0.324
2016 Marand AP, Zhang T, Zhu B, Jiang J. Towards genome-wide prediction and characterization of enhancers in plants. Biochimica Et Biophysica Acta. PMID 27321818 DOI: 10.1016/j.bbagrm.2016.06.006  0.474
2015 Zhang T, Marand AP, Jiang J. PlantDHS: a database for DNase I hypersensitive sites in plants. Nucleic Acids Research. PMID 26400163 DOI: 10.1093/nar/gkv962  0.418
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