Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： doi.org/10.3389/fpls.2024.1339594

Language：English   Publishing type：Research paper (scientific journal)  

DOI： doi.org/10.1186/s13073-023-01270-8

Language：English   Publishing type：Research paper (scientific journal)   Publisher：BMC  

Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea.

DOI： 10.1186/s13059-021-02475-z

Language：English   Publishing type：Research paper (scientific journal)  

<h4>Background</h4>Testing strategies is crucial for genetics clinics and testing laboratories. In this study, we tried to compare the hit rate between solo and trio and trio plus testing and between trio and sibship testing. Finally, we studied the impact of extended family analysis, mainly in complex and unsolved cases.<h4>Methods</h4>Three cohorts were used for this analysis: one cohort to assess the hit rate between solo, trio and trio plus testing, another cohort to examine the impact of the testing strategy of sibship genome vs trio-based analysis, and a third cohort to test the impact of an extended family analysis of up to eight family members to lower the number of candidate variants.<h4>Results</h4>The hit rates in solo, trio and trio plus testing were 39, 40, and 41%, respectively. The total number of candidate variants in the sibship testing strategy was 117 variants compared to 59 variants in the trio-based analysis. We noticed that the average number of coding candidate variants in trio-based analysis was 1192 variants and 26,454 noncoding variants, and this number was lowered by 50-75% after adding additional family members, with up to two coding and 66 noncoding homozygous variants only, in families with eight family members.<h4>Conclusion</h4>There was no difference in the hit rate between solo and extended family members. Trio-based analysis was a better approach than sibship testing, even in a consanguineous population. Finally, each additional family member helped to narrow down the number of variants by 50-75%. Our findings could help clinicians, researchers and testing laboratories select the most cost-effective and appropriate sequencing approach for their patients. Furthermore, using extended family analysis is a very useful tool for complex cases with novel genes.

DOI： 10.1186/s12920-020-00743-8

Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Genetics Society of America  

DOI： 10.1534/g3.119.400864

Language：English   Publishing type：Rapid communication, short report, research note, etc. (scientific journal)   Publisher：Cold Spring Harbor Laboratory  

<jats:title>Abstract</jats:title><jats:p>Despite an increasing gain of knowledge regarding small extracellular vesicle (sEV) composition and functions in cell-cell communication, the mechanism behind their biogenesis remains unclear. Here, we revealed for the first time that the sEV biogenesis and release into the microenvironment are tightly connected with another important organelle: Lipid Droplets (LD). We have observed this correlation using different human cancer cell lines as well as patient-derived colorectal cancer stem cells (CR-CSCs). Our results showed that the use of external stimuli such as radiation, pH, hypoxia, or lipid interfering drugs, known to affect the LD content, had a similar effect in terms of sEV secretion. Additional validations were brought using multiple omics data, at the mRNA and protein levels. Altogether, the possibility to fine-tune sEV biogenesis by targeting LDs, could have a massive impact on the amount, the cargos and the properties of those sEVs, paving the way for new clinical perspectives.</jats:p><jats:sec><jats:title>Significance Statement</jats:title></jats:sec>

DOI： 10.1101/2022.10.24.513202

Event date： 2023.12

Language：English   Presentation type：Poster presentation  

Venue：神戸ポートアイランド  

Event date： 2023.1

Language：English   Presentation type：Poster presentation  

Venue：San Diego  

Event date： 2022.12

Language：English   Presentation type：Oral presentation (invited, special)  

Event date： 2020.12

Language：English   Presentation type：Oral presentation (general)  

Event date： 2014.7

Language：English   Presentation type：Oral presentation (general)