GENE EXPRESSION
My lab
participated to the sequencing of the
Vitis vinifera genomes, and then performed a number of
microarray analyses
of genome wide gene expression for grapevine functional studies. As 2nd/Next Generation Sequencing
technologies (NGS) gained popularity for transcriptome analysis because
of their ability
to generate digital and quantitative information and to discover
previously
unknown genes, in 2008 we embraced gene expression analysis
based on deep
sequencing of the transcriptome (RNA-Seq). Since then, my lab
has continued
implementing and developing new wet-lab methodologies and
bioinformatic
pipelines for expression data analysis on genomic scales.
GENOME ASSEMBLY AND HUMAN GENOME SEQUENCING
As
the sequencing costs
dropped, we begun involved in sequencing a number of bacterial,
fungal and
plant genomes. With surprise, we found that our experience
on sequencing
assembling and annotating the genome of "difficult" fungi and
plants
allowed us to smoothly approach human whole genome sequencing
(WGS) and
interpretation. Thanks to a lab composed by fantastic and
enthusiastic
people with different skills and very much different backgrounds
(bioengineers,
human and plant bioinformaticians, computer scientists,
biotechnologists and
geneticists), we are now taking full advantage of our
understanding of the
complexity of different living organisms. It's amazing to
see how much it
can be learned when in the same lab people work on bacteria,
plants and humans.
A striking example is the comparison of genetic diversity in
plant and humans:
due to the young age (~60.000 years), to the fact that
population has rapidly
increased in the last 200 years or so (we were a 1 billion in
1800, 2 billion
in 1930 and now increase a billion every 10-12 years) and to the
continuous
moving (and mating) of people all over the world, human genetic
diversity is
much limited compared to plants. Vitis vinifera for
instance, like
Arabidopsis and poplar, is a dicotyledonous plant that diverged
from
monocotyledons about 130–240 Myr ago. Being propagated
asexually, each variety
maintains a genetic diversity that goes beyond simple allele
variation.
ON-SITE SEQUENCING
I love technologies. Comparison of the different genomic technologies currently available and testing of
new emerging technologies for DNA sequencing and analysis is an integral
part of our mission that has allowed us to bring a genomics lab where the samples are, instead of bringing the samples to the lab. This paradigm shift required a tremendous effort as we had to make "mobile" many technologies, forcing us to develop a
"lateral
thinking" approach.
LATERAL THINKING
The term "Lateral thinking" was coined in 1967 by Edward de
Bono. Lateral thinking is solving problems through an
indirect and creative
approach, using reasoning that is not immediately obvious and
involving ideas
that may not be obtainable by using only traditional
step-by-step logic.
Lateral thinking deliberately distances itself from standard
perceptions of
creativity as either "vertical" logic (the classic method for
problem
solving: working out the solution step-by-step from the given
data) or
"horizontal" imagination (having a thousand ideas but being
unconcerned with the detailed implementation of them). Lateral thinking is now an integral component of our
scientific approach.
Obviously, as we critically evaluate and discuss every single
step of
genome/transcriptome sequencing and data analysis, there is no
room for
"kit-persons" in the lab.