[Comp-neuro] 'la Caixa' INPhINIT PhD opportunity at MCEN/BCAM and UChicago on neuron-glial connectomics

Maurizio De Pitta mdepitta at bcamath.org
Thu Nov 29 16:05:06 CET 2018

Dear colleagues,
please share with whoever could be interested and forward to your
department mailing lists.

PhD project : Structure and function of the glial connectome.

Lab / Host institution : Group of Mathematical, Computational and
Experimental Neuroscience (MCEN) at the Basque Center of Applied
Mathematics (BCAM).
Supervisors : Maurizio De Pittà (BCAM), SerafimRodrigues (BCAM),
Narayanan Kasthuri (The University of Chicago, and Argonne National
Location : Bilbao, The Basque Country, Spain.
Duration : 3 years.
Stipend : 30k+ EUR/year + mobility allowance.
Starting date : May—Oct 2019 (negotiable).
Award type: Preselection + competitive call.
Categories: Incoming (for international students not living in Spain
at the time of the call) and Retaining (for Spanish students)
Preselection deadline: January 13th, 2019 (incoming); February 9th,
2019 (retaining).
Application deadlines: February 6th, 2019 (incoming); February 27th,
2019 (retaining) (more details: https://goo.gl/HZCPxp)

Scientific background :
Neurons of the brain form complex circuits, connecting each other by
means of synapses. The structure of these circuits is believed to
closely relate with their function. Accordingly, mapping the
architecture of neural circuits of the brain, otherwise known as the
brain’s neuronal connectome, is a prominent area of investigation of
modern neuroscience. In parallel, there is growing awareness that
glial cells such as astrocytes, could modulate the physical structure
of the neuronal connectome. Astrocytes indeed form barriers to
neuronal connectivity and regulate synapse formation and deletion, but
they could also modulate neuronal signal transmission in the
extracellular space, along with structure and dynamics of synapses. In
addition, astrocytes contact hundreds of thousand synapses, and are
also connected in complex networks. This suggests that understanding
the neuronal connectome should also include neuron-astrocyte
interactions and thus mapping of the associated glial connectome in
terms of synapse-astrocyte and astrocyte-astrocyte connections.

Workplan :
The candidate will be part of an international team of researchers
within the framework of the Open Connectome Project
(https://neurodata.io/). She/He will deploy mathematical tools
borrowed from graph theory, statistical analysis, machine learning and
algebraic topology to analyze big data sets from 3D electron
microscopy of cortical tissue of rodent’s brain to seek the first map
of astrocytic connections with synapses at subcellular spatial
resolution. In parallel the candidate will develop expertise in
modeling of complex heterogeneous cell networks of neurons and
astrocytes, to explore potential functional relevance of specific
synapse-astrocyte circuits and motifs in neuron-glial networks.

Working environment :
The candidate will be based in Bilbao (Spain) where she/he will work
under the supervision of Drs. Maurizio De Pittà and Serafim Rodrigues
at the Group of Mathematical, Computational and Experimental
Neuroscience at the Basque Center of Applied Mathematics (BCAM). In
addition, the candidate will also collaborate with and be supervised
by Dr. Narayanan “Bobby” Kasthuri at the University of Chicago and
Argonne National Labs (USA), where she/he will spend regular periods
of time during her/his graduate training. Dr. De Pittà is a leading
expert on computational modeling of neuron-glia interactions, with an
experience in computational neuroscience of 10+ years who recently
joined the MCEN group at BCAM as « Junior Leader » fellow with a
start-up grant supported by la Caixa Banking Foundation. The MCEN
group is a rapidly growing team led by Ikerbasque Professor Serafim
Rodrigues, that was established in 2016 as part of the strategic
research portfolio enacted by the Basque Country to foster
interdisciplinary research in Neuroscience. Dr. Kasthuri is one of the
leading experts in modern connectomics, who has pioneered large volume
automated electron microscopy for mapping neuronal connections and
synchrotron source X-ray microscopy to map the cellular composition of
entire brains. BCAM is one of the Severo Ochoa’s excellence centers
for scientific research in Spain and it provides an exeptionally
fertile international environment for professional development and
enriching scientific collaborations. Bilbao, as the capital of the
Basque Country in Spain, is a vibrant, friendly city with one of the
highest standards of life quality in Spain.

Requirements :
-- Master’s degree (or equivalent) in Physics, Mathematics,
Engineering, or related fields.
-- Excellent English skills (oral and written).
– Experience in machine learning and/or statistical analysis and/or
topology or algebraic topology.
-- Programming skills in Matlab, Python and C/C++.
-- High motivation for interdisciplinary research with strong
interests for biological details and an analytic mindset.
– Capacity to meet deadlines and outstanding propensity to work in an
international dynamic environment.
-- Essential knowledge of neuroscience and graph theory is preferred
but not required.

Additional notes :
This is a cutting-edge project that ideally matches with outstanding
and creative candidates, with a strong motivation for international
collaborations, mobility, and independence. The candidate will work on
the project full-time and no part-time agreements will be taken into

Application process :
The INPhINIT PhD Fellowship Program by la Caixa Banking Foundation is
the most prestigious PhD fellowship program running in Spain. The
program is highly competitive and offers unequalled training an
financial support to its fellow. The ideal successful candidate should
have an outstanding educational background and rank among the 5% best
of his/her class. Candidates who are interested in the advertised PhD
project, must first send a CV with letter of motivation (max 2 pages)
to Drs. De Pittà (mdepitta at bcamath.org) and Kasthuri
(bobbykasthuri at uchicago.edu) for review and preselection.
Preselections are open now till January 13, 2019 (for incoming
candidates) and February 3rd, 2019 (for retaining candidates). Specify
as mail object: “INPhINIT PhD Project Application”.

Relevant References:
De Pittà et al., Astrocytes: orchestrating synaptic plasticity?,
Neuroscience, 2015, 323:43.
Katshuri et al., Saturated reconstruction of a volume of neocortex,
Cell, 2015, 162 :648

Relevant links:
Official call by BCAM: https://goo.gl/Vq8mto
INPhINIT: https://goo.gl/d761sP
BCAM homepage: https://goo.gl/ENSBAo
Maurizio De Pittà: https://goo.gl/pJXEYJ
Narayanan “Bobby” Kasthuri: https://goo.gl/pYmv2w
Open Connectome Project: https://neurodata.io/

Maurizio De Pitta'
Research Fellow
MCEN -- Group of Mathematical, Computational and Experimental Neuroscience
BCAM -- Basque Center of Applied Mathematics

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