👋 Hello! I’m Quentin Andres 👨💻, a second-year PhD candidate in Fisheries Science and Technology at Kasetsart University.
👉 My research focuses on the intersection of aquatic animal health, molecular biology, and genomics. Specifically, I aim to develop sustainable and low-cost vaccines 💉 for aquaculture, with a current focus on Streptococcus iniae 🦠 affecting Asian seabass 🐟. The methodologies I employ have potential applicability to a wider range of aquatic vertebrates and bacterial pathogens.
My thesis is organized into multiple facets, including:
🔎 The initial phase of my research was conducted under the Laboratory of Aquatic Animal Health Management and the Center of Excellence in Aquatic Animal Health Management, both housed within the Faculty of Fisheries at Kasetsart University.
📝 My first research article,“Comparative Genomics and Reverse Vaccinology of Streptococcus iniae: Blueprints for Affordable Aquaculture Vaccines,” introduces a novel framework for more affordable vaccines by integrating epidemiology, pan-genomics, and reverse vaccinology, coupled with Quality By Design (QbD) principles and will soon be published..
I’m committed to advancing the fields of aquaculture genomics and aquatic health management with focus on Asian aquaculture 🌏🎣.
Inactivated vaccines: Developed and evaluted oral-oil-encapsulated and immersion monovalent and bivalent vaccines for Streptococcus agalactiae and Aeromonas veronii for Nile tilapia. Found that for those formulations specifically, immersion was more effective in conferring protective efficacy for a few months and that oral vaccines were more appropriate to be given as a booster after primer vaccination.
mRNA vaccines: Explored mRNA vaccine design and manufacturing against TiLV for Nile tilapia (Project stalled)
Experience Levels
🟩🟩🟩🟩🟩 R
🟩🟩🟩🟩🟨 Bash-command line
🟩🟩🟩🟨🟨 Python
🟩🟩🟨🟨🟨 Perl
Download My Résumé. (coming soon..)
👉 Feel free to 📩 email me for collaborations or discussions.
You can also find me on 🤝 LinkedIn, 💻 Github and check out some of my publications in my 🌐 academic page below.
The following facet presents the different skills that I master or very familiar with:
In-silico cloning (DNA Cauldron)
PyDNA
Snapgene
NEB Golden Gate Tool
Benchling
PCR
In-vivo assembly cloning
Golden Gate Assembly cloning
Separation of DNA by gel-electrophoresis
Purification of nucleic acid sequences (gDNA)
Purification of nucleic acid sequences (pDNA)
Purification of nucleic acid sequences (RNA)
Recombination & mutagenesis
Transcriptional fusions
Bacterial transformations
DNA probe hybridization on nitrocellulose membrane
qRT-PCR
qPCR
Preparation of culture media for Escherichia coli
Gram-staining
Bacterial transformations
Cellular culture (animal)
MTT Assay
Trypan blue assay
Transfection
Propidium Iodide assay
Fluorescence microscopy
Confocal microscopy
Purification of proteins by affinity to GST
SDS-PAGE
BCA assay
Bradford assay
Western blot
ELISA & ELISPOT
RefSeq
UniprotKB
RegulonDB
VICTORS
VFDB
PATRIC
Immune Epitope Database (IEDB)
NCBI
EBI
GenBank
Ensembl
NCBI entrez
JSON
XML
SQL
Kraken2
SeqAdapt
SeqPurge
Trimmomatic
Awk
seqtk
FastQC
QUAST
Bandage
Unicycler
SPAdes
Mauve
Mummer
Bowtie2
Picard
Bamtools
bcftools
PILON
Velvet
Snippy
BWA-MEM
fastANI
QUAST
Mash
Integrated Genome Viewer (IGV)
PopPUNK
fastbaps
GrapeTree
Microreact
DBScan
KNN
K-means clustering
Prokka
PGAP
CRISPRTyper
ISmapper
PanISa
BEDTools
BoBro2.0
GOST
KEGG
KRONA
Progressive Mauve
Progressive Cactus
PhyML
IQ-Tree 2
ggtree
Ape
Phytools
Castor
Gubbins
ClonalFrameML
HyPhy
vg Toolkit
ODGI
PGGB
vg (Sequence Tube Maps)
Roary
Piggy
panX
Pandora
Panaroo
Cytoscape
ForceAtlas2
PPanGGOLiN
MAFFT
Clustal Omega
Diamond
BLAST
SKA2
Bowtie2
INTERPROSCAN
TIGRFAM
SIGNALIP
PRINTS
Pfam
Antifam
TMHMM
MobiDBLite
eggNOG 6.0
Circos
R Suite
Bioconductor
Github
GNU parallel
Understanding of data structures
Inference and Modeling
Data Wrangling
Exploratory Data Analysis
Linear Regression
Principal component analysis
Comprehensive analysis of up-to-date public knowledge on recombinant protein vaccines
Protein expression systems
Protein purification systems
Vaccine efficacy
Bioprocess optimization
Quality by Design (QbD)
Comprehensive analysis of up-to-date public knowledge on plasmid DNA vaccines
Vector design
Optimization of expression
pDNA purification methods
Bioprocess scale-up
Vaccine efficacy
Quality by Design (QbD)
Comprehensive analysis of up-to-date public knowledge on pan-genomics and of Firmicutes
Comparative genomics and functional genomics
Streptococcus Mutans, Bovis, Pyogenic group
Streptococcus iniae
Streptoccocus agalactiae (GBS)
Streptococcus pyogenes (GAS)
ggplot2
ggpubr
dplyr
tidyverse
plotly
Markdown
Blogdown
Shiny
I am familiar with those topics to a certain point and have ever raised juveniles and adult Nile Tilapia during vaccine trials
Recirculating Aquaculture Systems
Aquaponics systems
Biofloc systems
Hatchery technologies
Catfish farming
Carp farming
Tilapia farming
Shrimp farming
Seafood business
Fish nutrition
Feed formulation design
Farm design
Sustainable aquaculture and SDGs
French native
English fluent
Thai (ภาษาไทย) B2
Spanish B1
Slovak A2
The high cost of vaccines relative to antimicrobials in aquaculture limits their adoption, particularly in low-value freshwater fish that nonetheless play a crucial role in global food security. Current vaccines, killed or live attenuated are highly effective but are no longer cost-efficient. Here, we present a new framework that leverages epidemiology, pangenomics, and reverse vaccinology with Quality By Design (QbD) principles to design more affordable vaccines. Targeting a range of aquatic streptococcal species, we emphasize the fish pathogen Streptococcus iniae. We identify a subset of protein antigens from the proteome that are well-adapted for low-cost mass production using QbD manufacturing strategies. This integrated approach is a crucial step towards making vaccines more accessible and cost-effective for global aquaculture, ultimately aiding in combating antimicrobial resistance and ensuring food security and consumer health.
Summary presentation of my PhD thesis for the part on genome sequencing and Analysis, comparative genomics of Streptococcus iniae and explaining about the manufacturing strategies of recombinant proteins vaccines (pDNA vaccines are not included..)
Aquaculture has made significant strides in providing a sustainable and efficient protein source. However, bacterial infections such as those caused by Streptococcus agalactiae and Aeromonas veronii remain a persistent challenge, affecting the health and productivity of Nile tilapia (Oreochromis niloticus) fingerlings. This study aimed to assess and compare the efficacy of two bivalent inactivated vaccines administered through different methods: oral vaccine followed by an oral booster (OR+OR) and immersion vaccine followed by an oral booster (IM+OR).