Research

Biomedical Research – mechanisms of cell-state transitions

Taking a highly data-driven approach, the overarching goal of my research is a deeper understanding of the molecular mechanisms driving cellular-state transitions in health and disease. I am particularly interested in how the interactions between transcription factors and non-coding regions of the genome regulate the expression of genes, with a view to gaining quantitative insights into the causes of aberrant gene expression in disease.

During my fellowship, my work has focussed on quantifying the neccessary molecular changes required for the stable formation of the mammalian eye-field – the earliest known stage of eye development. The main goal of my research is to identify how a key set of eye-field transcription factors is switched-on in a coordinated manner in the developing neural plate during gastrulation.

In order to build data-driven evidence and hypotheses of these critical mechanisms, I develop and apply machine learning methods to extract informative patterns from bulk and single-cell genomic datasets (mainly RNA-seq and ATAC-seq) generated from primary tissue and model systems.

Two key projects I am currently leading on are:

• Characterising the mammalian eye-field state using an organoid model.
  Using integrated analyses of matched RNA-seq and ATAC-seq time-course data from mESC-derived optic-vescicle organoids, we develop a systematic approach to identify candidate transcription factors and cis-regulatory elements important for controlling gene-expression programs crucial for enabling cells to transition to ocular states.
  [with L. Owen & D. FitzPatrick: now on bioRxiv!]

• Coupled transcriptome-chromatin dynamics and regulation of cell state in early eye development.
  Developing computational approaches for analyses of 10X single-cell Multiome data, aiming to reveal generalizable principles of chromatin-accessibility regulated gene-expression and cell differentiation, during eye-field specification.
  [Awarded an Wellcome/UoE ISSF grant to generate data and develop methods for this project.]

Biology/Biomedical Pre-prints

Biology/Biomedical Publications (peer reviewed)

Unique functions of two overlapping PAX6 retinal enhancers
K. Uttley, A.S. Papanastasiou, M. Lahne, J.M. Brisbane, R.B. MacDonald, W.A. Bickmore and S. Bhatia
Life Science Alliance (2023) 6 (11), e202302126 [doi] [bioRxiv]

Characterization of an Eye Field-like State during Optic Vesicle Organoid Development
L.J. Owen, J. Rainger, H. Bengani, F. Kilanowski, D.R. FitzPatrick and A.S. Papanastasiou
Development (2023) 150 (15), dev201432 [doi] [bioRxiv]

Robust genetic analysis of the X-linked anophthalmic (Ie) mouse.
B.A. Hernandez-Moran, A.S. Papanastasiou, D. Parry, A. Meynert, P. Gautier, G. Grimes, I. Adams, V. Trejo-Reveles, H. Bengani, M. Keighren, I. Jackson, D.J. Adams, D.R. FitzPatrick and J. Rainger
Genes (2022) 13 (10), 1797 [doi] [bioRxiv]

Physics research summary (pre-2019)

I was lucky to work in Particle Physics during the hugely exciting time surrounding the discovery of the Higgs Boson at the experiments at CERN. My work during this time focused on improving theoretical predictions for hadron-collider processes involving heavy quarks, with particular emphasis on gaining better control of the underlying modelling uncertainties. The latter is a crucial step towards the precise extraction of Standard Model parameters from experimental data, as well as for aiding New Physics discoveries.

More specifically, in collaboration with many brilliant scientists and working within the framework of perturbative QCD, I developed new theoretical methods and simulation tools that directly resulted in more precise theory predictions and modelling for processes involving top and bottom quarks. I also worked on designing analyses with which to exploit experimental data so as to better extract fundamental parameters such as the top-quark mass and decay-width and the strong coupling constant.

Physics Publications (peer reviewed)

Note: by convention and with rare exceptions, authors in Particle Physics publications are listed in alphabetical order.

An exploratory study of the impact of CMS double-differential top distributions on the gluon parton distribution function.
M. Czakon, S. Dulat, T.-J. Hou, J. Huston, A. Mitov, A.S. Papanastasiou, I. Sitiwaldi, Z. Yu and C.-P. Yuan
J.Phys.G 48 (2021) 1, 015003 [doi] [arxiv]

Impact of LHC top-quark pair measurements to CTEQ-TEA PDF analysis.
O. Amat, M. Czakon, S. Dulat, T.-J. Hou, J. Huston, A. Mitov, A.S. Papanastasiou, C. Schmidt, I. Sitiwaldi, K. Xie, Z. Yu, C.-P. Yuan
PoS DIS2019 (2019) 017 – DIS2019 conference [doi] [arxiv]

(contribution to) Report from Working Group 1 : Standard Model Physics at the HL-LHC and HE-LHC.
P. Azzi, S. Farry, P. Nason et al.
CERN Yellow Rep.Monogr. 7 (2019) 1-220 [doi] [arxiv]

Top quark pair production at NNLO+NNLL’ in QCD combined with electroweak corrections.
M. Czakon, A. Ferroglia, A. Mitov, D. Pagani, A.S. Papanastasiou, B.D. Pecjak, D.J. Scott, I. Tsinikos, X. Wang, L.L. Yang, M. Zaro
Chin.Phys.C 44 (2020) 8, 083104, TOP2018 conference [doi] [arxiv]

Higher order corrections to spin correlations in top quark pair production at the LHC.
A. Behring, M. Czakon, A. Mitov, A.S. Papanastasiou and R. Poncelet
Phys.Rev.Lett. 123 (2019) 8, 082001 [doi] [arxiv]

NNLO versus NLO multi-jet merging for top-pair production including electroweak corrections.
M. Czakon, C. Gütschow, J.M. Lindert, A. Mitov, D. Pagani, A.S. Papanastasiou, M. Schönherr, I. Tsinikos and M. Zaro
TOP2018 conference [doi] [arxiv]

Top Quark Pair Production: theory overview.
A.S. Papanastasiou
TOP2017 conference [doi] [arxiv]

Heavy-flavor parton distributions without heavy-flavor matching prescriptions.
V. Bertone, A. Glazov, A. Mitov, A.S. Papanastasiou and M. Ubiali
JHEP 04 (2018) 046 [doi] [arxiv]

Fully-differential predictions for top pair-production and decay at high precision.
A.S. Papanastasiou
PoS(EPS-HEP2017)456 [doi] [arxiv]

Top-quark pair-production and decay at high precision.
J. Gao and A.S. Papanastasiou
Phys.Rev. D96 (2017) no.5, 051501 [doi] [arxiv]

(contribution to) Handbook of LHC Higgs Cross Sections: 4. Deciphering the Nature of the Higgs Sector.
D.~de Florian, C.~Grojean, F.~Maltoni et al.
CERN Yellow Reports: Monographs: Vol 2 (2017) [doi] [arxiv]

Matched predictions for the $bar{b}H$ cross section at the 13 TeV LHC.
M. Bonvini, A.S. Papanastasiou and F.J. Tackmann
JHEP 1610 (2016) 053 [doi] [arxiv]

Off-shell single-top production at NLO matched to parton showers.
S. Frixione, R. Frederix, A.S. Papanastasiou, S. Prestel and P. Torrielli
JHEP 1606 (2016) 027 [doi] [arxiv]

Theory overview of recent progress on single-top production predictions and tools.
A.S. Papanastasiou
PoS(TOP2015)22 [doi] [arxiv]

Probing the top-quark width through ratios of resonance contributions of $e^+e^- ightarrow W^+W^-bar{b}$.
S. Liebler, G. Moortgat-Pick, A.S. Papanastasiou
JHEP 1603 (2016) 099 [doi] [arxiv]

Resummation of b-quark mass effects in $bar{b}H$-induced Higgs production.
M. Bonvini, A.S. Papanastasiou and F.J. Tackmann
JHEP 1511 (2015) 196 [doi] [arxiv]

Renormalization-group improved fully differential cross sections for top pair production.
A. Broggio, A.S. Papanastasiou and A. Signer
JHEP 1410 (2014) 98 [doi] [arxiv]

(contribution to) High precision fundamental constants at the TeV scale.
S. Moch, S. Weinzierl et al.
Mainz Institute for Theoretical Physics (MITP) [doi] [arxiv]

Single-top $t$-channel production with off-shell and non-resonant effects.
A.S. Papanastasiou, R. Frederix, S. Frixione, V. Hirschi and F. Maltoni
Phys. Lett. B726 (2013) 223-227 [doi] [arxiv]

Finite-width effects in unstable-particle production at hadron colliders.
P. Falgari, A.S. Papanastasiou and A. Signer
JHEP 1305 (2013) 156 [doi] [arxiv]

Physics Pre-prints

Simultaneous extraction of $lpha_s$ and $m_t$ from LHC $tar{t}$ differential distributions
A.M. Cooper-Sarkar, M. Czakon, M.A. Lim, A. Mitov, A.S. Papanastasiou
2020 [arxiv]