ELFT HÍRADÓ

[Gergely J Szöllősi <sszolo AT gmail.com>]

Postdoc, senior postdoc, and scientific programmer positions are available at 
the Model-Based Evolutionary Genomics Unit at the Okinawa Institute of 
Science and Technology:

Postdoc:
https://www.oist.jp/careers/postdoctoral-position-model-based-evolutionary-genomics-unit

Senior postdoc:
https://www.oist.jp/careers/staff-scientist-senior-postdoc-model-based-evolutionary-genomics-unit

Scientific programmer:
https://www.oist.jp/careers/scientific-programmer-research-technician-model-based-evolutionary-genomics-unit

Join the Model-Based Evolutionary Genomics Unit 
(https://www.oist.jp/research/research-units/modevolgenom/) making 
fundamental contributions to research at the intersection of computational 
and evolutionary biology. Our unit works to decode the complex patterns and 
processes that underpin the evolution of life across its myriad forms with a 
significant focus on reconstructing the Tree of Life and modeling the 
dependency between different levels of organization in biological systems. By 
employing probabilistic models and leveraging the power of machine learning, 
we aim to unravel the co-evolutionary dynamics that have shaped the Tree of 
Life, from the enigmatic origins of early life forms to the sophisticated 
structures of modern biological systems. 

Current topics include:

 • applying and developing phylogenetically-aware models of horizontal gene 
transfer in order to reconstruct eukaryogenesis and better understand gene 
transfer in eukaryotes;

 • applying and developing molecular dating methods that use novel sources of 
timing information from transfers and correlations between phenotypes and 
ancient environments;

 • reconstructing ancient phenotypes from genome-scale data using machine 
learning;

 • adapting protein language models to reconstruct fitness landscapes and 
ancestral sequences;

 • understanding somatic evolution in hierarchically organized tissues and 
across the Tree of Life from a theoretical standpoint (e.g., To what extent 
has tissue organization evolved to minimize somatic evolution in humans? Why 
do both plants and animals have stem cells?)   

A position at the Model-Based Evolutionary Genomics Unit offers the freedom 
to pursue your own research ideas. It provides a platform for innovation and 
discovery in a unit that thrives on intellectual curiosity and 
interdisciplinary collaboration. The position includes funding,  provided by 
the budget of the Model-based Evolutionary Genomics Unit, to travel to 
international conferences as well as extended research visits to 
international collaborators, including Tom Williams at the University of 
Bristol, Anja Spang at NIOZ in the Netherlands, Phil Hugenholtz at the 
University of Queensland, and others.

Responsibilities (postdoc and senior postdoc):

Devise and lead state-of-the-art interdisciplinary research in Evolutionary 
Biology, and have fun doing it! Supervise team members including PhD students 
and postdocs. Maintain and develop new collaborations with researchers at 
OIST and other Universities, including the University of Bristol and the 
University of Queensland, NIOZ in the Netherlands, and the Institute of 
Evolution in Budapest. Publish results in leading journals and present them 
at international conferences. Application for independent funding is 
encouraged but not required.  

Some recent papers of ours:

“A rooted phylogeny resolves early bacterial evolution” Coleman, Davin, 
Mahendrarajah, Szánthó, Spang, Hugenholtz*, Szöllősi*, Williams*
Science 2021
https://science.sciencemag.org/content/372/6542/eabe0511.abstract

"Divergent genomic trajectories predate the origin of animals and fungi"
Ocaña-Pallarès, Williams, …, Bapteste, Tikhonenkov, Keeling, Szöllősi, 
Ruiz-Trillo
Nature 2022
https://www.nature.com/articles/s41586-022-05110-4

“Trade-off between reducing mutational accumulation and increasing commitment 
to differentiation determines tissue organization” Demeter, Derényi, Szöllősi
Nature Communications 2022
https://www.nature.com/articles/s41467-022-29004-1

“Compositionally Constrained Sites Drive Long-Branch Attraction ” Szánthó, 
Lartillot, Szöllősi*, Schrempf*
Systematic Biology 2023
https://doi.org/10.1093/sysbio/syad013

“AleRax: A tool for gene and species tree co-estimation and reconciliation 
under a probabilistic model of gene duplication, transfer, and loss” Morel, 
Williams, Stamatakis, Szöllősi
Bioinformatics 2024 (to appear)
https://doi.org/10.1101/2023.10.06.561091

Okinawa Institute of Science and Technology

The Okinawa Institute of Science and Technology Graduate University (OIST; 
see www.oist.jp) is a dynamic new graduate university of science and 
technology in Okinawa Prefecture, Japan. The university is located on 85 
hectares of protected forestland overlooking beautiful shoreline and coral 
reefs. The campus is striking architecturally, and the facilities are 
outstanding (OIST campus video tour: 
https://www.youtube.com/watch?v=OLeylXbZDpo). There are no academic 
departments, which facilitates multidisciplinary research. Outstanding 
resources and equipment are provided and managed to encourage easy access and 
collaboration. English is the official language of the University, and the 
university research community is fully international, with more than 50 
countries represented. OIST is rapidly gaining recognition in the worldwide 
academic community as a model for excellence in education and research.

How to Apply:

Please visit the above links for details or contact gergely.szollosi AT oist.jp.

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Dr. Gergely J Szöllősi

MTA-ELTE ,,Lendület”
Evolutionary Genomics Research Group
ERC “GENECLOCKS” Research Group
head researcher

Model-Based Evolutionary Genomics Unit
モデルベース進化ゲノミクスユニット
Okinawa Institute of Science and Technology
Transitional Associate Professor

http://ssolo.web.elte.hu
Tel: 00 36 30 725 35 32
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