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% Style file with biblatex options for ATLAS documents.
\usepackage[backref=false]{atlasbiblatex}

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\usepackage[jetetmiss, hepparticle]{atlasphysics}
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%          other, snippets
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% Add your own definitions here (file atlas-document-defs.sty).
\usepackage{PubCom_BibTeX-defs}

% Files with references in BibTeX format
\addbibresource{../../bib/ATLAS.bib}
\addbibresource{../../bib/CMS.bib}
\addbibresource{../../bib/ConfNotes.bib}
\addbibresource{../../bib/PubNotes.bib}
\addbibresource{../../bib/ATLAS-useful.bib}

% Paths for figures - do not forget the / at the end of the directory name.
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% Collect dates of last updates
\NewDocumentCommand{\exptDate}{}{2025-06-30}
\NewDocumentCommand{\IDDate}{}{2025-06-31}
\NewDocumentCommand{\egammaDate}{}{2025-07}
\NewDocumentCommand{\muonDate}{}{2025-07-26}
\NewDocumentCommand{\fakeDate}{}{no information}
\NewDocumentCommand{\jetDate}{}{2025-05-13}
\NewDocumentCommand{\metDate}{}{2025-05-13}
\NewDocumentCommand{\tauDate}{}{2025-07-23}
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\AtlasTitle{PubCom standard references}

\author{ATLAS Publication Committee Chairs}

\AtlasRefCode{Version \ATPackageVersion}

\AtlasAbstract{%
  This note contains standard references that should be used in ATLAS documents.
  The references can all be found in the standard ATLAS \BibTeX\ files
  provided by the \texttt{atlaslatex} package.
  This document supersedes the TWiki page: \ATLASTWikiProtect{PubComUsefulBibTex}.

  Editors of the document should follow the conventions described in \cref{sec:editor}.
}
% Author and title for the PDF file
\hypersetup{pdftitle={ATLAS standard references},pdfauthor={ATLAS PubCom chairs}}

%-------------------------------------------------------------------------------
% Main document
%-------------------------------------------------------------------------------
\begin{document}

\maketitle

\tableofcontents

% Add line numbers temporarily.
% \linenumbers

%===============================================================================
\chapter{Introduction}%
\label{sec:intro}
%===============================================================================

This page contains a number of \BibTeX\ entries for papers which are commonly referenced in ATLAS CONF notes and papers,
and recommended by the performance and physics groups.
For ATLAS publications the \BibTeX\ key is provided, simply type \verb|\cite{key}|, where \Option{key} is, for example, \Option{EXOT-2016-19}.
The \BibTeX\ files can be found within the \Package{atlaslatex} package or on the page
\url{https://atlas-po.docs.cern.ch/atlaslatex/references/}.
It is recommended to use the standard bibliography files instead of extracting the individual \BibTeX\ entries into your paper \File{bib} file,
since there may be updates, errata, etc.\ made to the standard \File{bib} files.
Using the latest version of the standard \File{bib} files before the final sign-off stage will avoid a number of late fixes to the references.

The references mentioned here can mostly be found in the \File{ATLAS.bib} and \File{ATLAS-useful.bib} files from the \Package{atlaslatex} package. 

%===============================================================================
\chapter[HEP experiments and accelerators]{HEP experiments and accelerators\\ \Large{Last update: \exptDate}}
\label{sec:experiment}
%===============================================================================

%-------------------------------------------------------------------------------
\section{Experiments}%
\label{sec:experiment:experiment}

\subsection{ATLAS}

\begin{itemize}
  \item \Bibkey{PERF-2007-01} in \File{ATLAS.bib}.
    % On Inspire \url{https://inspirehep.net/literature/796888}.
  \item For IBL in \Run{2}: \Bibkey{ATLAS-TDR-19} (which calls \Bibkey{ATLAS-TDR-19-addm} internally) and \Bibkey{PIX-2018-001} in \File{ATLAS.bib}.
    % On CDS \url{https://cds.cern.ch/literature/1291633} and Inspire \url{https://inspirehep.net/literature/1658490}.
  \item For \Run{3} configuration: \Bibkey{GENR-2019-02} in \File{ATLAS.bib}.
    % On Inspire \url{https://inspirehep.net/literature/2663519}.
\end{itemize}

\subsection{CMS}

\begin{itemize}
  \item \Bibkey{CMS-TDR-08-001} in \File{CMS.bib}.
    % On Inspire: \url{https://inspirehep.net/literature/796887}.
\end{itemize}

%-------------------------------------------------------------------------------
\section{Accelerators}%
\label{sec:experiment:accelerator}

\subsection{LHC}

\begin{itemize}
  \item \Bibkey{Evans:2008zzb} in \File{ATLAS-useful.bib}.
\end{itemize}

%-------------------------------------------------------------------------------
\section{Beam energy}%
\label{sec:experiment:beamenergy}

Papers that need to refer to the \qty{0.1}{\%} beam energy uncertainty, 
should refer to the following paper:
\begin{itemize}
  \item \Bibkey{PhysRevAccelBeams.20.081003} from \File{ATLAS-useful.bib}.
\end{itemize}

%-------------------------------------------------------------------------------
\section{Luminosity}%
\label{sec:experiment:luminosity}

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{1}}{Run 1}}

\begin{itemize}
  \item First publication including methods (2010 data)\\
    \Bibkey{DAPR-2010-01} in \File{ATLAS.bib}.
    % On Inspire: \url{https://inspirebeta.net/literature/884120}.

  \item Updated publication (2010 and 2011 data)\\
    \Bibkey{DAPR-2011-01} in \File{ATLAS.bib}.
    % On Inspire: \url{https://inspirehep.net/literature/1219960}.

  \item Most recent \Run{1} publication (2012 data)\\
    \Bibkey{DAPR-2013-01} in \File{ATLAS.bib}.
    % On Inspire: \url{https://inspirehep.net/literature/1481187}.
\end{itemize}

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2} and/or \texorpdfstring{\Run{3}}{Run 3}}

Please follow the recommendations from \ATLASTWiki{LuminosityForPhysics}.
For \pp data, the current recommendation is to quote the \Run{2} luminosity paper and the LUCID2 paper 

%-------------------------------------------------------------------------------
\section{Data Quality}%
\label{sec:experiment:dq}

\subsection{\texorpdfstring{\Run{2}}{Run 2} and/or \texorpdfstring{\Run{3}}{Run 3}}

Quote the \Run{2} data quality paper (\Bibkey{DAPR-2018-01} in \File{ATLAS.bib}) when mentioning data quality requirements.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]


%===============================================================================
\chapter[Inner Tracking]{Inner Tracking\\ \Large{Last update: \IDDate}}%
\label{sec:ID}
%===============================================================================

Public results from the ATLAS Tracking Performance Group are reported on this page: \ATLASTWikiPublic{InDetTrackingPerformanceApprovedPlots}.

The most relevant publications for every LHC run are reported below.

%-------------------------------------------------------------------------------
\section{Track reconstruction}%
\label{sec:ID:reconstruction}
%-------------------------------------------------------------------------------

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{1}}{Run 1}}

Performance of the ATLAS Inner Detector Track and Vertex Reconstruction in the High Pile-Up LHC Environment:\\
\Bibkey{ATLAS-CONF-2012-042} in \File{ConfNotes.bib}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2}}

Performance of the ATLAS Track Reconstruction Algorithms in Dense Environments in LHC \Run{2}
(track selections, performance, and efficiency uncertainties inside dense environments (jets, taus, etc)):\\
\Bibkey{PERF-2015-08} in \File{ATLAS.bib}.

Early Inner Detector Tracking Performance in the 2015 data at \(\sqrt{s} = \qty{13}{\TeV}\)
(track selections and inclusive tracking uncertainties including efficiency, fake rate, alignment, and impact parameters):\\
\Bibkey{ATL-PHYS-PUB-2015-051} in \File{PubNotes.bib}. 

Plots showing the impact of IBL distortions on the tracking can be found
\href{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PLOTS/IDTR-2015-009/}{here} and 
\href{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PLOTS/IDTR-2015-011/}{here}.

Comparison between 2012 \Run{1} and 2015 \Run{2} detector configuration for the transverse and longitudinal impact parameters,
mainly showing the impact of the IBL:\\
\Bibkey{GENR-2019-02} in \File{ATLAS.bib}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{3}}{Run 3}}
Performance of ATLAS Pixel Detector and Track Reconstruction at the start of \Run{3} in LHC Collisions at \(\sqrt{s} = \qty{900}{\GeV}\):\\
\Bibkey{ATL-PHYS-PUB-2022-033} in \File{PubNotes.bib}.

Track reconstruction software performance in \Run{3}:\\
\Bibkey{IDTR-2022-04} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2689672}.

Performance of the reconstruction of large impact parameter tracks in the inner detector of ATLAS:
\Bibkey{IDTR-2021-03} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2654056}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{4}}{Run 4}}

Expected Tracking Performance of the ATLAS Inner Tracker at the High-Luminosity LHC:\\
\Bibkey{IDTR-2023-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2861687}.

%-------------------------------------------------------------------------------
\section{Vertex reconstruction}
%-------------------------------------------------------------------------------

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{1}}{Run 1}}

Reconstruction of primary vertices at the ATLAS experiment in \Run{1} proton--proton collisions at the LHC\\
\Bibkey{PERF-2015-01} in \File{ATLAS.bib}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2}}

Vertex Reconstruction Performance:\\
\Bibkey{ATL-PHYS-PUB-2015-026} in \File{PubNotes.bib}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{3}}{Run 3}}

Development of ATLAS Primary Vertex Reconstruction for LHC \Run{3}:\\
\Bibkey{ATL-PHYS-PUB-2019-015} in \File{PubNotes.bib}.

Performance plots for the ATLAS Track and Vertex Reconstruction in early LHC \Run{3}:
\href{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PLOTS/IDTR-2022-08/}{plots}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{4}}{Run 4}}

Expected Tracking Performance of the ATLAS Inner Tracker at the High-Luminosity LHC:\\
\Bibkey{IDTR-2023-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2861687}.

%-------------------------------------------------------------------------------
\section{Alignment}%
\label{sec:ID:alignment}
%-------------------------------------------------------------------------------

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{1}}{Run 1}}

Alignment of the ATLAS Inner Detector and its Performance in 2012:\\
\Bibkey{ATLAS-CONF-2014-047} in \File{ConfNotes.bib}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2}}

Alignment of the ATLAS Inner Detector with the initial LHC data at 13 TeV:\\
\Bibkey{ATL-PHYS-PUB-2015-031} in \File{PubNotes.bib}. 

Plots showing the impact of IBL distortions on the alignment can be found
\href{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PLOTS/IDTR-2015-011/}{here}. 

Alignment of the ATLAS Inner Detector in \Run{2}:\\
\Bibkey{IDTR-2019-05} in \File{ATLAS.bib}.
% On Inspire: https://inspirehep.net/literature/1806928 

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{3}}{Run 3}}

Inner Detector alignment development and performance in preparation for \Run{3}:\\
\Bibkey{ATL-PHYS-PUB-2022-028} in \File{PubNotes.bib}.

%-------------------------------------------------------------------------------
\section{Material}%
\label{sec:ID:material}
%-------------------------------------------------------------------------------

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{1}}{Run 1}}

A measurement of material in the ATLAS tracker using secondary hadronic interactions in \qty{7}{\TeV} \pp collisions:\\
\Bibkey{PERF-2015-06} in \File{ATLAS.bib}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2}}

Study of the material of the ATLAS inner detector for \Run{2} of the LHC:\\
\Bibkey{PERF-2015-07} in \File{ATLAS.bib}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{4}}{Run 4}}

Expected Tracking Performance of the ATLAS Inner Tracker at the High-Luminosity LHC:\\
\Bibkey{IDTR-2023-01} in \File{ATLAS.bib}.
% On Inspire: https://inspirehep.net/literature/2861687 

%-------------------------------------------------------------------------------
\section{NN Clustering}%
\label{sec:ID:clustering}
%-------------------------------------------------------------------------------

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{1}}{Run 1}}

A neural network clustering algorithm for the ATLAS silicon pixel detector:\\
\Bibkey{PERF-2012-05} in \File{ATLAS.bib}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2}}

Training and validation of the ATLAS pixel clustering neural networks:\\
\Bibkey{ATL-PHYS-PUB-2018-002} in \File{PubNotes.bib}.

Performance of the ATLAS track reconstruction algorithms in dense environments in LHC \Run{2}:\\
\Bibkey{PERF-2015-08} in \File{ATLAS.bib}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{3}}{Run 3}}

Performance of charged-particle reconstruction in energetic jets for \Run{3} data taking with the ATLAS detector:
\href{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PLOTS/IDTR-2022-05/}{plots}.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Electrons and photons]{Electrons and photons\\ \Large{Last update: \egammaDate}}%
\label{sec:egamma}
%===============================================================================

The main standard references for electrons and photons reconstruction and identification, and the calibration, 
in ATLAS are cited below sorted by year/run period.

For \Run{3}, there are no new measurements or references that can be used,
and we suggest to write something along the following line(s) with the citations explained in more detail below:

\begin{quotation}
Electrons and photons are reconstructed as described in~\cite{EGAM-2018-01}.
They are calibrated based on the procedure and results described in~\cite{EGAM-2018-01,EGAM-2021-02}
with an additional correction on the in-situ scale and resolution corrections
that accounts for small differences in the ATLAS reconstruction software
and with increased uncertainties to reflect the \Run{3} pile-up conditions
and a change in optimal filtering coefficients for the LAr calorimeter readout.
Electrons are selected using the loose/medium/tight working points with loose/medium/xyz isolation
described in~\cite{EGAM-2021-01}.
Using the \PZ boson resonance and the methods described in~\cite{EGAM-2021-01}
preliminary data-to-MC correction factors were obtained 
with uncertainties slightly increased with respect to what is published in~\cite{EGAM-2021-01} for the full \Run{2}.
Photons are selected using the tight working point with loose/medium/xyz isolation
described in~\cite{EGAM-2021-01,EGAM-2018-01}.
Using radiative \PZ boson events as well as inclusive photons samples
a preliminary data-to-MC correction was obtained using the procedures described in~\cite{EGAM-2018-01}
with uncertainties slightly increased with respect to what is published in~\cite{EGAM-2021-01} for the full \Run{2}.
\end{quotation}

%-------------------------------------------------------------------------------
\section{Electron reconstruction}%
\label{sec:egamma:electron}
%-------------------------------------------------------------------------------

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{1}}{Run 1}}

Electron reconstruction+identification (Run1 data sliding window + GSF, 2012 data):\\
\Bibkey{PERF-2016-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1501691}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{{}\Run{2}}{Run 2} (rel.\ 20.7)}

Electron reconstruction (2015-2016 data, rel.\ 20.7 (sliding window)):\\
\Bibkey{PERF-2017-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1720078 }.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2} (rel.\ 21)}

Electron reconstruction (\Run{2} and \Run{3}, rel.\ \(\ge 21\) (super cluster)):\\
\Bibkey{EGAM-2018-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1747555}.

Electron efficiency (final \Run{2} rel.\ 21, ambient energy correction for isolation):\\
\Bibkey{EGAM-2021-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2691149}.

%-------------------------------------------------------------------------------
\section{Photon reconstruction}%
\label{sec:egamma:photon}
%-------------------------------------------------------------------------------

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{1}}{Run 1}}

Photon reconstruction and efficiency (\Run{1} data):\\
\Bibkey{PERF-2013-04} in \File{ATLAS.bib}.

Ambient Energy Correction to isolation energy:\\
\Bibkey{STDM-2010-08} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1091481}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2} (rel.\ 20.7)}

Photon reconstruction and efficiency (2015+2016 data, rel.\ 20.7 (sliding window cluster)):\\
\Bibkey{PERF-2017-02} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1698025}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{{\Run{2}}}{Run 2} (rel.\ 21)}

Photon reconstruction (\Run{2} and \Run{3}, rel.\ \(\ge 21\);
super cluster and includes conversions and electron/photon ambiguity resolver descriptions):\\
\Bibkey{EGAM-2018-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1747555}.

Photon efficiency (Final \Run{2} rel.\ 21):\\
\Bibkey{EGAM-2021-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2691149}.

%-------------------------------------------------------------------------------
\section{Electron and photon energy calibration}%
\label{sec:egamma:calib}
%-------------------------------------------------------------------------------

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{1}}{Run 1}}

Old calibration scheme and detector geometry (2010 data):\\
\Bibkey{PERF-2010-04} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/940010}

New calibration scheme and detector geometry (Run 1 data):\\
\Bibkey{PERF-2013-05} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1306905}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2} (rel.\ 20.7)}

\Run{2} calibration for rel.\ 20.7 (\Run{2} sliding window cluster):\\
\Bibkey{PERF-2017-03} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1707967}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2} (rel.\ 21)}

\Run{2} calibration for rel. 21 (\Bibkey{PERF-2017-03} is still relevant, and is quoted in this paper):\\
\Bibkey{EGAM-2018-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1747555}.

Final calibration for \Run{2} rel.\ 21:\\
\Bibkey{EGAM-2021-02} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2696998}.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Muons]{Muons\\ \Large{Last update: \muonDate}}%
\label{sec:muon}
%===============================================================================

A list of references can be found here:
\url{https://atlas-mcp.docs.cern.ch/publications/index.html}.

%-------------------------------------------------------------------------------
\section{Muon identification}%
\label{sec:muon:identifcation}
%-------------------------------------------------------------------------------

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run~2}{Run 2}}

\Bibkey{MUON-2018-03} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1834360}.

%-------------------------------------------------------------------------------
\section{Muon reconstruction}
\label{sec:muon:reconstruction}
%-------------------------------------------------------------------------------

\subsection{2015 data}

\Bibkey{PERF-2015-10} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1429662}.

\subsection{2011 and 2012 data}

\Bibkey{PERF-2014-05} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1306491}.

\subsection{2010 data}

\Bibkey{PERF-2011-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1291133}.

%-------------------------------------------------------------------------------
\section{Muon calibration}%
\label{sec:muon:calibration}
%-------------------------------------------------------------------------------

\subsection{\texorpdfstring{\Run~2}{Run 2}}

\Bibkey{MUON-2022-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2614209}.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Isolation and fake leptons]{Isolation and fake leptons\\ \Large{Last update: \fakeDate}}%
\label{sec:fake}
%===============================================================================

\Bibkey{EGAM-2019-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2605175}.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Jets]{Jets\\ \Large{Last update: \jetDate}}%
\label{sec:jet}
%===============================================================================

 All Jet/Etmiss publications can be found here: \url{https://twiki.cern.ch/twiki/bin/view/AtlasPublic/JetEtmissPublicResults}.
 Only recent, \Run{2} or \Run{3} related recommendations are listed below.
 Some techniques were documented in \Run{1} publications, which we leave here for reference.

%-------------------------------------------------------------------------------
\section{Jet reconstruction}%
\label{sec:jet:reconstruction}
%-------------------------------------------------------------------------------

\emph{Note: see below for references to jet algorithms and theory references.}

%-------------------------------------------------------------------------------
\subsection{Topological clusters}

\Bibkey{PERF-2014-07} in \File{ATLAS.bib}.
% On Inspire: https://inspirehep.net/record/1426830

%-------------------------------------------------------------------------------
\subsection{Particle flow}

\Bibkey{PERF-2015-09} in \File{ATLAS.bib}.
% On Inspire: https://inspirehep.net/literature/1520722

%-------------------------------------------------------------------------------
\subsection{UFO jets}

\Bibkey{JETM-2018-06} in \File{ATLAS.bib}.
% On Inspire: https://inspirehep.net/literature/1816107

%-------------------------------------------------------------------------------
\subsection{Cell timing cut in \topo reconstruction}

Run 3 analyses only:\\
\Bibkey{JETM-2023-01} in \File{ATLAS.bib}.
% On Inspire: https://inspirehep.net/literature/2713959

%-------------------------------------------------------------------------------
\section{Jet energy scale and resolution}%
\label{sec:jet:jesjer}
%-------------------------------------------------------------------------------

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{1}}{Run 1} pile-up mitigation techniques}

\Bibkey{PERF-2014-03} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/1397638}.

%-------------------------------------------------------------------------------
\subsection[Consolidated Run 2 JES/JER]{Consolidated \Run{2} JES/JER (2015-2017 data)}

Current reference for \Run{2} papers:\\
\Bibkey{JETM-2018-05} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1805279}.

%-------------------------------------------------------------------------------
\subsection[Run 2 large-radius in situ calibration]{\Run{2} large-radius in situ calibration}

Current reference for large-R JES/JMS calibration:\\
\Bibkey{JETM-2018-02} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1683827}.

%-------------------------------------------------------------------------------
\subsection{\texorpdfstring{\Run{2}}{Run 2} Large-radius JMS/JMR in situ calibration}

Current reference for large-R JMS/JMR calibration:\\
\Bibkey{ATLAS-CONF-2020-022} in \File{ConfNotes.bib}.
% On the web: \url{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/CONFNOTES/ATLAS-CONF-2020-022/}.

%-------------------------------------------------------------------------------
\section{Jet pile-up suppression (JVT, fJVT)}%
\label{sec:jet:pileup}
%-------------------------------------------------------------------------------

\subsection{JVT / NNJVT}

This is \Run{1} JVT paper to be cited for both, \Run{2} NNJVT paper is planned for early 2026:\\
\Bibkey{PERF-2014-03} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/1397638}.

\subsection{fJVT for EMTopo jets}

\Bibkey{PERF-2016-06} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1598265}.

\subsection{fJVT for PFlow jets}

\Bibkey{ATL-PHYS-PUB-2019-026} in \File{PubNotes.bib}.
% On the web: \url{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PUBNOTES/ATL-PHYS-PUB-2019-026/}.

%-------------------------------------------------------------------------------
\section{Jet substructure and tagging performance}%
\label{sec:jet:substructure}
%-------------------------------------------------------------------------------

\subsection[Run 2 W/top tagging performance]{\Run{2} \PW/top tagging performance}

Default reference for tagging in \Run{2}:\\
\Bibkey{JETM-2018-03} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1690929}.

\subsection[Run 2 W/top tagging scale factors]{\Run{2} \PW/top tagging scale factors}

Default reference for uncertainties + latest taggers in \Run{2}, use together with \Bibkey{JETM-2018-03}:
\Bibkey{ATL-PHYS-PUB-2020-017} in \File{PubNotes.bib}.
% On the web: \url{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PUBNOTES/ATL-PHYS-PUB-2020-017/}.

\subsection[Run 2 W/Z tagging scale factors for TCC jets]{\Run{2} \PW/\PZ tagging scale factors for TCC jets}

\Bibkey{ATL-PHYS-PUB-2020-008} in \File{PubNotes.bib}.
% On the web: \url{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PUBNOTES/ATL-PHYS-PUB-2020-008/}.

\subsection{\texorpdfstring{\Run{2}}{Run 2} Higgs tagging}

Please see FTAG recommendations for updates/calibration.\\
\Bibkey{PERF-2017-04} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/1741421}.

\subsection{Top tagging with UFO jets}

\Bibkey{ATL-PHYS-PUB-2021-028} in \File{PubNotes.bib}.
% On the web: \url{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PUBNOTES/ATL-PHYS-PUB-2021-028/}.

\subsection[W/Z tagging with UFO jets]{\PW/\PZ tagging with UFO jets}

\Bibkey{ATL-PHYS-PUB-2021-029} in \File{PubNotes.bib}.
% On the web: \url{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PUBNOTES/ATL-PHYS-PUB-2021-029/}.

\subsection{Performance of quark/gluon tagging in rel.\ 21}

\Bibkey{JETM-2020-02} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2684714}.

%-------------------------------------------------------------------------------
\section{Jet algorithms}%
\label{sec:jet:algorithm}
%-------------------------------------------------------------------------------

Make sure to cite FastJet in addition to the jet clustering algorithm to abide by the licensing agreement.

\Antikt algorithm\\
\Bibkey{Cacciari:2008gp} in \File{ATLAS-useful.bib}.

Fastjet\\
\Bibkey{Fastjet} in \File{ATLAS-useful.bib}.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Missing transverse momentum]{Missing transverse momentum\\ \Large{Last update: \metDate}}%
\label{sec:met}
%===============================================================================

%-------------------------------------------------------------------------------
\section[ETmiss performance in Run 2]{\MET performance in \Run{2}}
%-------------------------------------------------------------------------------

Reference for Run2 papers:\\
\Bibkey{JETM-2020-03} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/literature/2756722}.

%-------------------------------------------------------------------------------
\section[ETmiss significance in Run 2]{\MET significance in \Run{2}}
%-------------------------------------------------------------------------------

\Bibkey{ATLAS-CONF-2018-038} in \File{ConfNotes.bib}.
% On the web: \url{https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/CONFNOTES/ATLAS-CONF-2018-038/}.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Flavour tagging]{Flavour tagging\\ \Large{Last update: \flavourDate}}%
\label{sec:flavour}
%===============================================================================

Release 25: \href{https://atlas-talk.web.cern.ch/t/how-to-cite-gn2-in-a-paper/47314/2}{atlas-talk}\\
Legacy: \ATLASTWikiProtect{BTaggingPaperRecommendations}.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Taus]{Taus\\ \Large{Last update: \tauDate}}%
\label{sec:tau}
%===============================================================================

%-------------------------------------------------------------------------------
\section{Fake tau background estimation}
%-------------------------------------------------------------------------------

\Bibkey{TAUP-2023-01} in \File{ATLAS.bib}.

%-------------------------------------------------------------------------------
\section{Tau reconstruction and identification}
%-------------------------------------------------------------------------------

muonRM taus, both in \Run{2} and \Run{3}:\\
\Bibkey{TAUP-2023-02} in \File{ATLAS.bib}.

Boosted-ditau, both \Run{2} and \Run{3}:\\
\Bibkey{TAUP-2020-03} in \File{ATLAS.bib}.
\Bibkey{HDBS-2019-22} in \File{ATLAS.bib}.

%-------------------------------------------------------------------------------
\section{Tau identification algorithms (tauID)}
%-------------------------------------------------------------------------------

For \Run{2}, rel.\ 22 (reprocessed data) and \Run{3} analyses using tau-leptons:\\
\Bibkey{ATL-PHYS-PUB-2022-044} in \File{PubNotes.bib}.

For \Run{2} analyses (rel.\ 21) using the RNN TauID algorithm:\\
\Bibkey{ATL-PHYS-PUB-2019-033} in \File{PubNotes.bib}.

For \Run{2} analyses (rel.\ 21), the performance of the tauID algorithms and recommendations are described
on the TWiki page: \ATLASTWikiProtect{TauWG}.

The \Run{1} paper (listed below) can still be referenced in addition for a more detailed description of the algorithms
and of performance of the tau energy calibration.
\Bibkey{ATLAS-CONF-2017-029} in \File{ConfNotes.bib}.

A public document is available, summarising the tauID algorithms, and pre-recommendations.
It should be used for any result using the \Run{2} pre-recommendations:\\
\Bibkey{ATL-PHYS-PUB-2015-045} in \File{PubNotes.bib}.

%-------------------------------------------------------------------------------
\section[Run 1 tau performance]{\Run{1} tau performance}
%-------------------------------------------------------------------------------

The \Run{1} tau performance paper is the sole reference required for offline and online tau performance in \Run{1}.
The article covers reconstruction, energy calibration and identification plus the associated performance measurements.\\
\Bibkey{PERF-2013-06} in \File{ATLAS.bib}. 

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Trigger]{Trigger\\ \Large{Last update: \trigDate}}%
\label{sec:trigger}
%===============================================================================

A list of all references can be found here:
\ATLASTWikiPublic{TriggerPublicResults}.

Key publications are listed below.

%-------------------------------------------------------------------------------
\section{Trigger system publications}%
\label{sec:trigger:system}
%-------------------------------------------------------------------------------

If the paper uses any combination of \Run{1}, \Run{2} and \Run{3} data, please cite all applicable papers below.

%-------------------------------------------------------------------------------
\subsection[Run 1 data only]{\Run{1} data only}

Performance of the ATLAS Trigger System in 2010\\
\Bibkey{TRIG-2011-02} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/930968}.

%-------------------------------------------------------------------------------
\subsection[Run 2 data only]{\Run{2} data only}

Performance of the ATLAS Trigger system in 2015:\\
\Bibkey{TRIG-2016-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/1500696}.

%-------------------------------------------------------------------------------
\subsection[Run 3 data only]{\Run{3} data only}

The ATLAS Trigger System for LHC Run 3 and Trigger performance in 2022:\\
\Bibkey{TRIG-2022-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/2746398}.


%-------------------------------------------------------------------------------
\section{Trigger signature publications}%
\label{sec:trigger:signature}
%-------------------------------------------------------------------------------

In addition, please cite all of the relevant signature publications for the specific triggers you've used:

%-------------------------------------------------------------------------------
\subsection[Run 3 data]{\Run{3} data}

\Pqb-jet triggers: Optimization and Commissioning of the \(b\)-jet triggers for LHC Run 3:\\
\Bibkey{TRIG-2022-02} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/2870995}.

Multi-b-jet triggers: Fast b-tagging at the high-level trigger of the ATLAS experiment in LHC Run 3:\\
\Bibkey{TRIG-2022-03} in \File{ATLAS.bib}. 
% On Inspire: \url{https://inspirehep.net/record/2669599}.

%-------------------------------------------------------------------------------
\subsection[Run 2 data]{\Run{2} data}

Electron / Photon triggers: Performance of the electron and photon triggers of the ATLAS experiment during LHC \Run{2}\\
\Bibkey{TRIG-2018-05} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/1752312}.

Muon triggers: Performance of the ATLAS muon triggers in \Run{2}\\
\Bibkey{TRIG-2018-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/1793218}.

Missing ET triggers: Performance of the missing transverse momentum triggers for the ATLAS detector during \Run{2} data taking
\Bibkey{TRIG-2019-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/1796953}.

b-jet triggers: Performance of the ATLAS \Pqb-jet trigger in \pp collisions at \(\sqrt{s} = \qty{13}{\TeV}\)\\
\Bibkey{TRIG-2018-08} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/1867276}.

L1Topo triggers: Performance of the ATLAS Level-1 topological trigger in \Run{2}\\
\Bibkey{TRIG-2019-02} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirehep.net/record/1861846}.

For any other signatures, please refer to the previous publications,
e.g.\ for jets you can use the 2011 paper for the description of the FS jet finding. 

Unless all your triggers are pure calorimeter triggers, please also cite\\
Inner Detector based triggers: The ATLAS Inner Detector Trigger performance in \pp collisions at \qty{13}{\TeV} during LHC Run 2:\\
\Bibkey{TRIG-2019-03} in \File{ATLAS.bib}. 
% On Inspire: \url{https://inspirehep.net/record/1877469}.

In case you discuss operational matters of the \Run{2} trigger system, please cite this paper:

Operation of the ATLAS trigger system in Run 2:\\
\Bibkey{TRIG-2019-02} in \File{ATLAS.bib}. 
% On Inspire: \url{https://inspirehep.net/record/1808700}.
    
%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[PDFs]{PDFS\\ \Large{Last update: \PDFDate}}%
\label{sec:pdf}
%===============================================================================

%-------------------------------------------------------------------------------
\section{PDF4LHC recommendations}
%-------------------------------------------------------------------------------

\Bibkey{Butterworth:2015oua} in \File{ATLAS-useful.bib}.

%-------------------------------------------------------------------------------
\section{CTEQ5}
%-------------------------------------------------------------------------------

\Bibkey{Lai:1999wy} in \File{ATLAS-useful.bib}.

%-------------------------------------------------------------------------------
\section{CTEQ6}
%-------------------------------------------------------------------------------

\Bibkey{Pumplin:2002vw} in \File{ATLAS-useful.bib}.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Simulation]{Simulation\\ \Large{Last update: \MCDate}}%
\label{sec:mc}
%===============================================================================

%-------------------------------------------------------------------------------
\section{Monte Carlo generators}
%-------------------------------------------------------------------------------

Check the following document by PMG (shipped with the \Package{atlaslatex} package)
that contains references for many samples:\\
\url{https://gitlab.cern.ch/atlas-physics-office/atlaslatex/-/tree/master/template/MC_snippets}.

%-------------------------------------------------------------------------------
\section{Simulation tools}
%-------------------------------------------------------------------------------

\subsection{GEANT4}

\Bibkey{Agostinelli:2002hh} in \File{ATLAS-useful.bib}.

Note that the following paper describes the full and all the flavoUrs of fast simulation;
it can be used as a reference for both the ATLAS detector simulation and for Atlfast-II, for example:\\
\Bibkey{SOFT-2010-01} in \File{ATLAS.bib}.
% On Inspire: \url{https://inspirebeta.net/record/856179}.

If you wish to discuss the details of hadronic physics lists in Geant4,
please cite:\\
\Bibkey{Geant4PhysicsLists} in \File{ATLAS-useful.bib}.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Statistical analysis]{Statistical analysis\\ \Large{Last update: \statDate}}%
\label{sec:stat}
%===============================================================================

\section{Neyman-Pearson lemma}

\Bibkey{Neyman:1933wgr} in \File{ATLAS-useful.bib}.

\section[CLs method]{\(CL_s\) method}

\Bibkey{Junk:1999kv}  in \File{ATLAS-useful.bib}.

\Bibkey{Read:2002hq} in \File{ATLAS-useful.bib}.

\section{Profile likelihood method}

\Bibkey{Rolke:2004mj} in \File{ATLAS-useful.bib}.

\section{Asymptotic formulae and profile likelihood}

\Bibkey{Cowan:2010js} from \File{ATLAS-useful.bib}.

\section{RooFit}

\Bibkey{RooFit} from \File{ATLAS-useful.bib}.

\section{RooUnfold}

\Bibkey{Adye:2011gm} from \File{ATLAS-useful.bib}.

\section{TMVA}

\Bibkey{TMVA} from \File{ATLAS-useful.bib}.

\section{Keras}

\Bibkey{chollet2015keras} from \File{ATLAS-useful.bib}.

\section{HistFitter}

\Bibkey{Baak:2014wma} in \File{ATLAS-useful.bib}.

\section{BLUE}

When using the BLUE method, please cite at least\\
\Bibkey{Lyons:1988rp} in \File{ATLAS-useful.bib}.

If the method involves multiple observables, please cite in addition\\
\Bibkey{2003NIMPA.500..391V} in \File{ATLAS-useful.bib}.

The following two citations can also be added, especially if the iterative version of BLUE is used:
\Bibkey{DAGOSTINI1994306} in \File{ATLAS-useful.bib}

and

\Bibkey{Blobel:2003wa} in \File{ATLAS-useful.bib}.

Finally, if the blue.hepforge.org implementation is used, please cite:\\
\Bibkey{Nisius:2020jmf} and \Bibkey{Nisius:2014wua} in \File{ATLAS-useful.bib}.

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\chapter[Physics processes and cross sections]{Physics processes and cross sections\\ \Large{Last update: \physicsDate}}%
\label{sec:physics}
%===============================================================================

%-------------------------------------------------------------------------------
\section{Higgs}
%-------------------------------------------------------------------------------

The recommended list of Higgs theory papers to be used for ATLAS Higgs papers can be found at:\\
\ATLASTWikiProtect{HiggsCrossSection}.

%-------------------------------------------------------------------------------
\section{SUSY}
%-------------------------------------------------------------------------------

A set of standard SUSY references can be found at:\\
\ATLASTWikiProtect{StandardSUSYRefs}.

%-------------------------------------------------------------------------------
\section{Top-quark pairs}
%-------------------------------------------------------------------------------

A list of references for top-quark pair production can be be found at:\\
\url{https://twiki.cern.ch/twiki/bin/view/LHCPhysics/TtbarNNLO#Proposed_citation_and_list_of_re}.

The page includes useful numbers and parameterisations of the cross section.
The content of the page was agreed on by ATLAS and CMS.

%-------------------------------------------------------------------------------
\section{Physics modelling group}
%-------------------------------------------------------------------------------

A list of references and text snippets for MC generators are provided by the physics modelling group and can be found
in the atlaslatex MC snippets 

%-------------------------------------------------------------------------------
% Print the bibliography for this chapter.
\printbibliography[heading=subbibliography]

%===============================================================================
\appendix
\crefalias{chapter}{appendix}
\chapter{Notes for editors}%
\label{sec:editor}
%===============================================================================

Editors of this document should follow the following conventions:
\begin{itemize}
  \item Update the relevant chapter date at the top of the document when changes are made.
  \item Use the \Macro{Bibkey} command to refer to the \BibTeX\ keys in the text.
  \item Use the \Macro{File} command to refer to the \File{bib} files.
  \item Use the \Macro{Run} command to refer to the LHC runs.
    Note that if you use the command in a section title, you should either provide an alternative title
    in square brackets or use the \Macro{texorpdfstring} command to avoid warnings when making the PDF file.
  \item Use one of the commands \Macro{ATLASTWiki}, \Macro{ATLASTWikiPublic}, or \Macro{ATLASTWikiProtect} 
    to refer to the ATLAS TWiki pages.
\end{itemize}

% \cref{sec:editor} is the last chapter of this document.

\end{document}
