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Publications

Del-Bem Lab · Research output

Publications

Browse the laboratory’s publications, open each article through its original publisher link, and compare online attention, scholarly citations and related media coverage.

34publications

2009–2025publication years

14first- or corresponding-author publications

16published since 2020

Bold = Del-Bem Lab members · ^* co-first author · ^† corresponding author

34

Viral evolution & comparative genomics
Corresponding authorEditor’s Pick / Gems
Media & outreach

Mendonça-Santo T, Abrahão J, Del-Bem LE^†. (2025). Integrative genomic analyses support the division of the extended Asfarviridae clade into multiple viral families. Journal of Virology, 0:e01337-25, https://doi.org/10.1128/jvi.01337-25. [Editor’s Pick/Gems Section]

33

Plant defense proteins & molecular evolution
Book chapter

Pires LO*, Rodrigues WFC*, Del-Bem LE, Ishida Jk. (2024). Chapter 2: Origin and evolutionary history of defense-related proteins in plants. Book: Defense-Related Proteins in Plants. Academic Press (Elsevier), Pages 37-51, ISBN 9780443132360.

32

SARS-CoV-2 / transcriptomics & alternative splicing

Dias TL, Mamede I, de Toledo NE, Queiroz LR, Castro I, Polidoro R, Del-Bem LE, Nakaya H, Franco GR. (2024). SARS-CoV-2 Selectively Induces the Expression of Unproductive Splicing Isoforms of Interferon, Class I MHC, and Splicing Machinery Genes. Int. J. Mol. Sci., 25(11), 5671; https://doi.org/10.3390/ijms25115671.

31

Plant glycosyl hydrolases & horizontal gene transfer
Corresponding author
Media & outreach

Kfoury B, Rodrigues WFC, Kim SJ, Brandizzi F, Del-Bem LE^† (2024). Multiple horizontal gene transfer events have shaped plant glycosyl hydrolase diversity and function. New Phytologist, 242(2):809-824

30

Giant-virus genome evolution & gene duplication
Corresponding author

Machado TB, Picorelli ACR, de Azevedo BL, de Aquino ILM, Queiroz VF, Rodrigues RAL, Araújo Jr. JP, Ullmann LS, dos Santos TM, Marques RE, Guimarães SL, Andrade ACSP, Gularte JS, Demoliner M, Filippi M, Pereira VMAG, Spilki FR, Krupovic M, Aylward FO, Del-Bem LE^†, Abrahão JS^†. (2023). Gene duplication as a major force driving the genome expansion in some giant viruses. Journal of Virology, e01309-23.

29

Comparative genomics & bioinformatics

Hongo JA*, de Castro GM*, Menezes APA*, Picorelli ACR, da Silva TTM, Imada EL, Marchionni L, Del-Bem LE, Chaves AV, Almeida GMF, Campelo F, Lobo FP. (2023). CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species. Patterns, https://doi.org/10.1016/j.patter.2023.100728.

28

Iron uptake evolution & plant nutrition
Corresponding author
Media & outreach

Rodrigues WFC, Lisboa ABP, Lima JE, Ricachenevsky FK, Del-Bem LE^† (2023). Ferrous iron uptake via IRT1/ZIP evolved at least twice in green plants. New Phytologist, 237(6):1951-1961.

27

tRNA evolution & comparative genomics
Corresponding author

Santos FB, Del-Bem LE^† (2023). The Evolution of tRNA Copy Number and Repertoire in Cellular Life. Genes, 14(1):27. https://doi.org/10.3390/genes14010027.

26

Plant cell cycle & protein turnover

Strini EJ, Bertolino LT, San Martin JAB, Souza HAO, Pessotti F, Pinoti VF, Ferreira PB, De Paoli HC, Lubini G, Del-Bem LE, Quiapim AC, Mondin M, Araujo APU, Eloy NB, Barberis M, Goldman MHS (2022). Stigma/Style Cell-Cycle Inhibitor 1, a Regulator of Cell Proliferation, Interacts With a Specific 14-3-3 Protein and Is Degraded During Cell Division. Frontiers in Plant Science, 13:857745.

25

Skeletal-muscle hypertrophy & transcriptomics

Copola AGL, dos Santos IGD, Coutinho LL, Del-Bem LE, Campos-Junior PHA, da Conceição IMCA, Nogueira JM, Costa AC, Silva GAB, Jorge EC (2022). Transcriptomic characterization of the molecular mechanisms induced by RGMa during skeletal muscle nuclei accretion and hypertrophy. BMC Genomics, 23, 188.

24

SARS-CoV-2 / human variation & structural modeling
Corresponding author
Media & outreach

Santos TM^*, Lisboa ABP^*, Rodrigues W, Gomes H, Abrahão J, Del-Bem LE^† (2022). Human variation in the protein receptor ACE2 affects its binding affinity to SARS-CoV-2 in a variant-dependent manner. Journal of Biomolecular Structure and Dynamics, 1-9.

23

Fungal mitogenomics & genome evolution
Corresponding author

Fonseca PLC, De-Paula RB, Araújo DS, Tomé LMR, Mendes-Pereira T, Rodrigues WFC, Del-Bem LE^†, Aguiar ERGR, Góes-Neto, A (2021). Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements. Frontiers in Microbiology, 12:787283.

22

Ascorbate peroxidase evolution & Archaeplastida

Lazzarotto F, Menguer PK, Del-Bem LE, Zámocký M, Margis-Pinheiro M (2021). Ascorbate peroxidase neofunctionalization at the origin of APX-R and APX-L: evidence from basal Archaeplastida. Antioxidants, 10 (4), 597.

21

Fungal mitogenomics & ORF evolution

Araújo DS, De-Paula RB, Tomé LMR, Quintanilha-Peixoto G, Salvador-Montoya CA, Del-Bem LE, Badotti F, Azevedo VAC, Brenig B, Aguiar ERGR, Drechsler-Santos ER, Fonseca PLC, Góes-Neto A (2021). Comparative mitogenomics of Agaricomycetes: diversity, abundance, impact and coding potential of putative open-reading frames. Mitochondrion, Vol 58, Issue 5, 1-13

20

ADAM gene-family evolution & comparative genomics
Corresponding author
Media & outreach

Souza JSM^*, Lisboa ABP^*, Santos TM^*, Andrade MVS, Neves VBS, Teles-Souza J, Jesus HNR, Bezerra TG, Falcão VGO, Oliveira RC, Del-Bem LE^† (2020). The evolution of ADAM gene family in eukaryotes. Genomics, Vol 112, Issue 5, 3108-3116.

19

Fungal mitogenomics & genome architecture

Fonseca PLC, Badotti F, De-Paula RB, Araújo DS, Bortolini DE, Del-Bem LE, Azevedo VA, Brenig B, Aguiar ERGR, Góes-Neto A (2020). Exploring the Relationship Among Divergence Time and Coding and Non-coding Elements in the Shaping of Fungal Mitochondrial Genomes. Frontiers in Microbiology, 11:765.

18

Plant drought response & SOD gene-family evolution

Gomes Neto V, Ribeiro PR, Del-Bem LE, Bernal DT, Cunha Lima ST, Ligterink W, Fernandez LG, de Castro RD (2018). Characterization of the superoxide dismutase gene family in seeds of two Ricinus communis L. genotypes submitted to germination under water restriction conditions. Environmental and Experimental Botany. Vol 155, 453-463.

17

Xyloglucan evolution & plant terrestrialization
Corresponding authorViewpoint
First authorMedia & outreach

Del-Bem LE^† (2018). Xyloglucan evolution and the terrestrialization of green plants. New Phytologist. 219(4): 1150–1153

16

Plant–pathogen interactions & functional genomics

de Almeida DSM, do Amaral DOJ, Del-Bem LE, dos Santos EB, Silva RJS, Gramacho KP, Vincentz M, Micheli F (2017). Genome-wide identification and characterization of cacao WRKY transcription factors and analysis of their expression in response to witches’ broom disease. PLoS One, 12 (10), e0187346.

15

Sugarcane polyploidy & genome evolution
Co-first authorMedia & outreach

Vilela MM^*, Del-Bem LE^*, Van Sluys MA, de Setta N, Kitajima JP, Cruz GM, Sforça DA, de Souza AP, Ferreira PC, Grativol C, Cardoso-Silva CB, Vicentini R, Vincentz M. (2017). Analysis of Three Sugarcane Homo/Homeologous Regions Suggests Independent Polyploidization Events of Saccharum officinarum and Saccharum spontaneum. Genome Biology & Evolution, 9(2):266-278.

14

Sugarcane genomics & genome evolution
Media & outreach

De Setta N, Monteiro-Vitorello CB, Metcalfe CJ, Cruz GM, Del Bem LE, Vicentini R, Nogueira FT, Campos RA, Nunes SL, Turrini PC, et al (2014). Building the sugarcane genome for biotechnology and identifying evolutionary trends. BMC Genomics, 15:540.

13

Plant epigenetics & de novo gene evolution

Silveira, AB, Trontin C, Cortijo S, Barau J, Del Bem LEV, Loudet O, Colot V, Vincentz M (2013). Extensive natural epigenetic variation at a de novo originated gene. PLoS Genetics, 9:e1003437.

12

Sugarcane transcriptomics & ncRNA genomics
Co-first author

Vicentini R^*, Del Bem LEV^*, Van Sluys MA, Nogueira FTS, Vincentz M (2012). Gene content analysis of sugarcane public ESTs reveals thousands of missing coding-genes and an unexpected pool of grasses conserved ncRNAs. Tropical Plant Biology, 5:199-205.

11

Microbial stress proteins / phylogenetics & structural modeling

Ribeiro DA, Del Bem LEV, Vicentini R, Ferraz LFC, Murakami MT, Ottoboni LMM (2011). The small heat shock proteins from Acidithiobacillus ferrooxidans: gene expression, phylogenetic analysis, and structural modeling. BMC Microbiology, 11:259.

10

Plant signaling & transcriptional regulation

Matiolli CC, Tomaz J, Duarte GT, Prado FM, Del Bem LEV, Silveira AB, Gauer L, Corrêa LGG, Drumond RD, Viana AJC, Di Mascio P, Meyer C, Vincentz M (2011). The Arabidopsis bZIP gene AtbZIP63 is a sensitive integrator of transient abscisic acid and glucose signals. Plant Physiology, 157:692-705.

9

Calreticulin/calnexin evolution & plant genomics
Corresponding author
First author

Del Bem LEV^† (2011). The evolutionary history of calreticulin and calnexin genes in green plants. Genetica, 139:255-259.

8

Seed proteomics

Campos FAP, Nogueira F, Cardoso KC, Costa GCL, Del Bem LEV, Domont GB, Da Silva MJ, Moreira RC, Soares AA, Jucá TL (2010). Proteome analysis of castor bean seeds. Pure and Applied Chemistry, 82:259-267.

7

Venom-gland transcriptomics

Cardoso KC, Da Silva MJ, Costa GGL, Torres TT, Del Bem LEV, Vidal RO, Menossi M, Hyslop S (2010). A transcriptomic analysis of gene expression in the venom gland of the snake Bothrops alternatus (urutu). BMC Genomics, 11:605.

6

Sugarcane microRNAs & functional genomics

Zanca AS, Vicentini R, Ortiz-Morea FA, Del Bem LEV, da Silva MJ, Vincentz M, Nogueira FTS (2010). Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane. BMC Plant Biology, 10:260.

5

Xyloglucan evolution & comparative genomics
Corresponding author
First authorMedia & outreach

Del Bem LEV^†, Vincentz MGA (2010). Evolution of xyloglucan-related genes in green plants. BMC Evolutionary Biology, 10:341.

4

Seed transcriptomics & bioenergy
Co-first author

Costa GGL^*, Cardoso KC^*, Del Bem LEV^*, Lima AC, Cunha MAS, de Campos-Leite L, Vicentini R, Papes F, Moreira RC, Yunes JA, Campos FAP, Da Silva MJ (2010). Transcriptome analysis of the oil-rich seed of the bioenergy crop Jatropha curcas L. BMC Genomics, 11:462.

3

Paleobotany & fossil anatomy

de Faria RS, Ricardi-Branco F, Giannini PCF, Sawakuchi AO, Del Bem LEV (2009). Lycopodiopsis derbyi Renault from the Corumbataí Formation in the state of São Paulo (Guadalupian of Paraná Basin, Southern Brazil): New data from compressed silicified stems. Review of Palaeobotany and Palynology, 158:180-192.

2

Sugarcane functional genomics & sucrose metabolism

Papini-Terzi FS, Rocha FR, Vêncio RZN, Felix JM, Branco DS, Waclawovsky AJ, Del Bem LEV, Lembke CG, Costa MDL, Nishiyama MY, Vicentini R, Vincentz MGA, Ulian EC, Menossi M, Souza GM (2009). Sugarcane genes associated with sucrose content. BMC Genomics, 10:120.

1

Seedling development & xyloglucan metabolism

Brandão AD, Del Bem LEV, Vincentz M, Buckeridge MS (2009). Expression pattern of four storage xyloglucan mobilization-related genes during seedling development of the rain forest tree Hymenaea courbaril L. Journal of Experimental Botany, 60:1191-1206.