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Documents authored by Martens, Lennart

Document
DOI: 10.4230/DagRep.13.7.152
Computational Proteomics (Dagstuhl Seminar 23301)

Authors: Rebekah Gundry, Lennart Martens, and Magnus Palmblad

Published in: Dagstuhl Reports, Volume 13, Issue 7 (2024)

Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 23301 "Computational Proteomics". This seminar was built around three topics: the increasingly widespread use, and continously increasing promise of advanced machine learning approaches in proteomics; the highly exciting, yet fiendishly complicated, field of single cell proteomics, and the development of novel computational methods to analyse the highly challenging data obtained from the glycoproteome. These three topics fuelled three parallel breakout sessions, which ran in parallel at any given time throughout the seminar. A fourth, cross-cutting breakout session was created during the seminar as well, which dealt with the standardisation efforts in proteomics data, and explored the possibilities to upgrade these standards to better cope with the increasing demands being put on the relevant data storage and dissemination formats. This report comprises an Executive Summary of the Dagstuhl Seminar, which describes the overall seminar structure together with the key take-away messages for each of the three topics. This is followed by the abstracts, comprising three introduction talks, one for each topic, which were intended to whet the participants' appetite for each topic, while also introducing an expert perspective on the current challenges and opportunities in that topic. Along with the topic talks, two ad-hoc talks were presented during the seminar as well, and their abstracts are provided next. Moreover, each breakout session also comes with its own abstract, which provides insights into its discussions and relevant outcomes throughout the seminar.
Cite as

Rebekah Gundry, Lennart Martens, and Magnus Palmblad. Computational Proteomics (Dagstuhl Seminar 23301). In Dagstuhl Reports, Volume 13, Issue 7, pp. 152-165, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{gundry_et_al:DagRep.13.7.152,
  author =	{Gundry, Rebekah and Martens, Lennart and Palmblad, Magnus},
  title =	{{Computational Proteomics (Dagstuhl Seminar 23301)}},
  pages =	{152--165},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2024},
  volume =	{13},
  number =	{7},
  editor =	{Gundry, Rebekah and Martens, Lennart and Palmblad, Magnus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.13.7.152},
  URN =		{urn:nbn:de:0030-drops-197788},
  doi =		{10.4230/DagRep.13.7.152},
  annote =	{Keywords: bioinformatics, glycoproteomics, machine learning, mass spectrometry, proteomics, single cell proteomics}
}
Document
DOI: 10.4230/DagRep.11.6.1
Computational Proteomics (Dagstuhl Seminar 21271)

Authors: Sebastian Böcker, Rebekah Gundry, Lennart Martens, and Magnus Palmblad

Published in: Dagstuhl Reports, Volume 11, Issue 6 (2021)

Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 21271 "Computational Proteomics". The Seminar, which took place in a hybrid fashion with both local as well as online participation due to the COVID pandemic, was built around three topics: the rapid uptake of advanced machine learning in proteomics; computational challenges across the various rapidlly evolving approaches for structural and top-down proteomics; and the computational analysis of glycoproteomics data. These three topics were the focus of three corresponding breakout sessions, which ran in parallel throughout the seminar. A fourth breakout session was created during the seminar, on the specific topic of creating a Kaggle competition based on proteomics data. The abstracts presented here first describe the three introduction talks, one for each topic. These talk abstracts are then followed by one abstract each per breakout session, documenting that breakout’s discussion and outcomes. An Executive Summary is also provided, which details the overall seminar structure alongside the most important conclusions for the three topic-derived breakouts.
Cite as

Sebastian Böcker, Rebekah Gundry, Lennart Martens, and Magnus Palmblad. Computational Proteomics (Dagstuhl Seminar 21271). In Dagstuhl Reports, Volume 11, Issue 6, pp. 1-13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@Article{bocker_et_al:DagRep.11.6.1,
  author =	{B\"{o}cker, Sebastian and Gundry, Rebekah and Martens, Lennart and Palmblad, Magnus},
  title =	{{Computational Proteomics (Dagstuhl Seminar 21271)}},
  pages =	{1--13},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2021},
  volume =	{11},
  number =	{6},
  editor =	{B\"{o}cker, Sebastian and Gundry, Rebekah and Martens, Lennart and Palmblad, Magnus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.11.6.1},
  URN =		{urn:nbn:de:0030-drops-155775},
  doi =		{10.4230/DagRep.11.6.1},
  annote =	{Keywords: bioinformatics, computational mass spectrometry, machine learning, proteomics}
}
Document
DOI: 10.4230/DagRep.9.8.70
Computational Proteomics (Dagstuhl Seminar 19351)

Authors: Nuno Bandeira and Lennart Martens

Published in: Dagstuhl Reports, Volume 9, Issue 8 (2020)

Abstract
This report documents the program and the outcomes of Dagstuhl Seminar 19351 ``Computational Proteomics''. The Seminar was originally built around four topics, identification and quantification of DIA data; algorithms for the analysis of protein cross-linking data; creating an online view on complete, browsable proteomes from public data; and detecting interesting biology from proteomics findings. These four topics were led to four correpsonding breakout sessions, which in turn led to five offshoot breakout sessions. The abstracts presented here first describe the four topic introduction talks, as well as a fifth, cross-cutting topic talk on bringin proteomics data into clinical trials. These talk abstracts are followed by one abstract each per breakout session, documenting that breakout's discussion and outcomes. An Executive Summary is also provided, which details the overall seminar structure, the relationship between the breakout sessions and topics, and the most important conclusions for the four topic-derived breakouts.
Cite as

Nuno Bandeira and Lennart Martens. Computational Proteomics (Dagstuhl Seminar 19351). In Dagstuhl Reports, Volume 9, Issue 8, pp. 70-83, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@Article{bandeira_et_al:DagRep.9.8.70,
  author =	{Bandeira, Nuno and Martens, Lennart},
  title =	{{Computational Proteomics (Dagstuhl Seminar 19351)}},
  pages =	{70--83},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2019},
  volume =	{9},
  number =	{8},
  editor =	{Bandeira, Nuno and Martens, Lennart},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.9.8.70},
  URN =		{urn:nbn:de:0030-drops-117724},
  doi =		{10.4230/DagRep.9.8.70},
  annote =	{Keywords: computational biology, computational mass spectrometry, proteomics}
}
Document
DOI: 10.4230/DagRep.7.10.69
Computational Proteomics (Dagstuhl Seminar 17421)

Authors: Bernhard Küster, Kathryn Lilley, and Lennart Martens

Published in: Dagstuhl Reports, Volume 7, Issue 10 (2018)

Abstract
The Dagstuhl Seminar 17421 "Computational Proteomics" discussed in-depth the current challenges facing the field of computational proteomics, while at the same time reaching out across the field's borders to engage with other computational omics fields at the joint interfaces. The ramifications of these issues, and possible solutions, were first introduced in short but thought-provoking talks, followed by a plenary discussion to delineate the initial discussion sub-topics. Afterwards, working groups addressed these initial considerations in great detail.
Cite as

Bernhard Küster, Kathryn Lilley, and Lennart Martens. Computational Proteomics (Dagstuhl Seminar 17421). In Dagstuhl Reports, Volume 7, Issue 10, pp. 69-83, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@Article{kuster_et_al:DagRep.7.10.69,
  author =	{K\"{u}ster, Bernhard and Lilley, Kathryn and Martens, Lennart},
  title =	{{Computational Proteomics (Dagstuhl Seminar 17421)}},
  pages =	{69--83},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2018},
  volume =	{7},
  number =	{10},
  editor =	{K\"{u}ster, Bernhard and Lilley, Kathryn and Martens, Lennart},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.7.10.69},
  URN =		{urn:nbn:de:0030-drops-86639},
  doi =		{10.4230/DagRep.7.10.69},
  annote =	{Keywords: computational biology, computational mass spectrometry, integrative bioinformatics, large scale public data, proteomics}
}
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