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Scopus Author ID: 6602556107

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Switzerland

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Employment (3)

SIB Swiss Institute of Bioinformatics: Lausanne, CH

2024-07-01 to present | Director (SIB Training Group)
Employment
Source: Self-asserted source
Patricia M. Palagi

Swiss Institute of Bioinformatics: Lausanne, VD, CH

2013-03-01 to present | Head of Training (SIB Training Group)
Employment
Source: Self-asserted source
Patricia M. Palagi

SIB Swiss Institute of Bioinformatics: Lausanne, CH

1997-05-01 to 2013-11-15 | Training coordinator, senior scientist, trainer (Proteomics Informatics Group)
Employment
Source: Self-asserted source
Patricia M. Palagi

Works (50 of 60)

Items per page:
Page 1 of 2

Using Glittr.org to find, compare and re-use online materials for training and education

PLOS ONE
2024-12-05 | Journal article
DOI: 10.1371/journal.pone.0308729
Contributors: Geert van Geest; Anna Bernasconi; Yann Haefliger; Monique Zahn-Zabal; Patricia M. Palagi
Source: check_circle
Crossref

A research data management (RDM) community for ELIXIR [version 2; peer review: 2 approved]

2024-09-30 | Journal article
DOI: 10.12688/f1000research.146301.2
Part of ISSN: 2046-1402
Funded by GRANT_NUMBER:

802750

Funded by GRANT_NUMBER:

871075
Contributors: Flora D'Anna; Niclas Jareborg; Mijke Jetten; Minna Ahokas; Pinar Alper; Robert Andrews; Korbinian Bösl; Teresa D’Altri; Daniel Faria; Nazeefa Fatima et al.
Source: check_circle
F1000

Using Glittr.org to find, compare and re-use online materials for training and education

2024-08-22 | Preprint
DOI: 10.1101/2024.08.20.608021
Contributors: Geert van Geest; Yann Haefliger; Monique Zahn-Zabal; Patricia M. Palagi
Source: check_circle
Crossref

BY-COVID D6.1 Stakeholder engagement report

Zenodo
2024-07-24 | Report
DOI: 10.5281/ZENODO.12820912
Contributors: Corinne Martin; Erika Balsyte; Andrea Guzmán Mesa; Carola Schulz; Despoina Sousoni; Vasso Kalaitzi; Simon Saldner; Aitana Neves; Dimitra Kondyli; Irena Vipavc Brvar et al.
Source: Self-asserted source
Patricia M. Palagi

BY-COVID D6.2 Training efforts report

Zenodo
2024-07-23 | Report
DOI: 10.5281/ZENODO.13349254
Contributors: Patricia Palagi; Nadim Rahman; Mari Kleemola; Vasso Kalaitzi; Simon Saldner; Helena Rasche; Isabel Marinna Kemmer; Sarah Morgan; Irena Vipavc Brvar
Source: Self-asserted source
Patricia M. Palagi

The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity [version 2; peer review: 3 approved]

2024-05-22 | Journal article
DOI: 10.12688/f1000research.133724.2
Part of ISSN: 2046-1402
Funded by GRANT_NUMBER:

22.00173

Funded by GRANT_NUMBER: PP00P3_202669
Contributors: Robert M. Waterhouse; Anne-Françoise Adam-Blondon; Bachir Balech; Endre Barta; Physilia Ying Shi Chua; Valeria Di Cola; Katharina F. Heil; Graham M. Hughes; Lars S. Jermiin; Matúš Kalaš et al.
Source: check_circle
F1000

Data sharing and reuse under GDPR - BY-COVID Fest workshop report

2024-05-20 | Report
DOI: 10.5281/ZENODO.11220597
Contributors: Simon Saldner; Sonja Bezjak; Vasso Kalaitzi; Dimitra Kondyli; Carola Schulz; Irena Vipavc Brvar; Patricia M. Palagi
Source: Self-asserted source
Patricia M. Palagi

Swiss Research Data Support Network (SRDSN)

Zenodo
2024-03-25 | Working paper
DOI: 10.5281/ZENODO.10869338
Contributors: Dirk Verdicchio; Silke Bellanger; Felix Moerman; Massimiliano Cannata; Igor Sarman; Jennifer Dean; Chiara Gabella; Patricia Palagi; Rita Gautschi; Mathilde Panes
Source: Self-asserted source
Patricia M. Palagi

Ten simple rules for writing a PLOS Computational Biology quick tips article

PLOS Computational Biology
2023-12-21 | Journal article
DOI: 10.1371/journal.pcbi.1011689
Contributors: Patricia M. Palagi; Feilim Mac Gabhann; Russell Schwartz; Scott Markel; B. F. Francis Ouellette
Source: check_circle
Crossref

Beyond COVID - how the BY-COVID project is increasing European pandemic preparedness

2023-11-27 | Preprint
DOI: 10.5281/ZENODO.10204209
Contributors: Katharina Lauer; Romain David; Jonathan Ewbank; Nina Van Goethem; Elaine Harrison; Niklas Blomberg; Enrique Bernal-Delgado; Philip Quinlan; Patricia Palagi; Susanna-Assunta Sansone et al.
Source: Self-asserted source
Patricia M. Palagi
grade
Preferred source (of 2)‎

An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond

PLOS ONE
2023-11-09 | Journal article
DOI: 10.1371/journal.pone.0293879
Part of ISSN: 1932-6203
Contributors: Jason Williams; Rochelle E. Tractenberg; Bérénice Batut; Erin A. Becker; Anne M. Brown; Melissa Burke; Ben Busby; Nisha Cooch; Allissa A. Dillman; Samuel S. Donovan et al.
Source: Self-asserted source
Patricia M. Palagi

Bioschemas Training profiles at the SIB Swiss Institute of Bioinformatics

Zenodo
2023-10-23 | Lecture
DOI: 10.5281/ZENODO.10070022
Contributors: Patricia M. Palagi
Source: Self-asserted source
Patricia M. Palagi

Building Research Data Management (RDM) expertise and training resources in ELIXIR Nodes

1st Conference on Research Data Infrastructure (CoRDI) - Connecting Communities
2023-09-12 | Conference abstract
DOI: 10.5281/ZENODO.8348286
Contributors: Celia W.G. Van Gelder; Patricia Palagi; Alexia Cardona; Brane Leskošek
Source: Self-asserted source
Patricia M. Palagi

Grand challenges in bioinformatics education and training

Nature Biotechnology
2023-08 | Journal article
DOI: 10.1038/s41587-023-01891-9
Contributors: Esra Büşra Işık; Michelle D. Brazas; Russell Schwartz; Bruno Gaeta; Patricia M. Palagi; Celia W. G. van Gelder; Prashanth Suravajhala; Harpreet Singh; Sarah L. Morgan; Hilyatuz Zahroh et al.
Source: check_circle
Crossref

LLMs for teaching – a game changer

31st Annual Intelligent Systems For Molecular Biology and the 22nd Annual European Conference on Computational Biology
2023-07-25 | Conference abstract
DOI: 10.5281/ZENODO.8187885
Contributors: Patricia M. Palagi
Source: Self-asserted source
Patricia M. Palagi

Bioschemas training profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources

PLOS Computational Biology
2023-06-15 | Journal article
DOI: 10.1371/journal.pcbi.1011120
Contributors: Leyla Jael Castro; Francis Ouellette; Patricia M. Palagi; Niall Beard; Teresa K. Attwood; Michelle D. Brazas
Source: check_circle
Crossref

Open data to support European pandemic preparedness.

2023-05-16 | Report
DOI: 10.5281/ZENODO.7950479
Contributors: Niklas Blomberg; Marieke Willems; Corinne S. Martin; Andy Smith; Elaine Harrison; Jose-Maria Carazo; Enrique Bernal-Delgado; Iris Van Dam; Romain David; Patricia M. Palagi et al.
Source: Self-asserted source
Patricia M. Palagi

Bioschemas Training Profiles: A set of specifications for standardizing training information to facilitate the discovery of training programs and resources

2022-11-29 | Preprint
DOI: 10.1101/2022.11.24.516513
Contributors: Leyla Jael Castro; Patricia M. Palagi; Niall Beard; Teresa K. Attwood; Michelle D. Brazas
Source: check_circle
Crossref

Community-driven ELIXIR activities in single-cell omics [version 1; peer review: 2 approved with reservations]

2022-07-29 | Journal article
DOI: 10.12688/f1000research.122312.1
Part of ISSN: 2046-1402
Funded by GRANT_NUMBER: http://dx.doi.org/10.13039/501100004063
Contributors: Paulo Czarnewski; Ahmed Mahfouz; Raffaele A. Calogero; Patricia M. Palagi; Laura Portell-Silva; Asier Gonzalez-Uriarte; Charlotte Soneson; Tony Burdett; Barbara Szomolay; Pavankumar Videm et al.
Source: check_circle
F1000
grade
Preferred source (of 2)‎

Using the The Mastery Rubric for Bioinformatics – A professional guide

F1000Research
2022-07-05 | Manual
DOI: 10.7490/F1000RESEARCH.1119023.1
Contributors: Patricia M. Palagi; Allegra Via; Patricia M. Palagi; Jessica M. Lindvall; Teresa K. Attwood; The GOBLET Foundation
Source: Self-asserted source
Patricia M. Palagi

Introducing the The Mastery Rubric for Bioinformatics – a Professional Guide

F1000Research
2022-07-04 | Manual
DOI: 10.7490/F1000RESEARCH.1119019.1
Contributors: Patricia M. Palagi; Allegra Via; Patricia M. Palagi; Jessica M. Lindvall; Teresa K. Attwood; The GOBLET Foundation
Source: Self-asserted source
Patricia M. Palagi

Ten simple rules for good research practice

PLOS Computational Biology
2022-06-23 | Journal article
DOI: 10.1371/journal.pcbi.1010139
Contributors: Simon Schwab; Perrine Janiaud; Michael Dayan; Valentin Amrhein; Radoslaw Panczak; Patricia M. Palagi; Lars G. Hemkens; Meike Ramon; Nicolas Rothen; Stephen Senn et al.
Source: check_circle
Crossref

Copyright Guidelines - How to acknowledge and be acknowledged in training material

SIB Swiss Institute of Bioinformatics
2021-11-29 | Manual
DOI: 10.5281/zenodo.5723925
Contributors: Patricia M. Palagi; Frédéric Schutz; Valeria Di Cola; Clément Parisato
Source: Self-asserted source
Patricia M. Palagi

Ten simple rules for good research practice

2021-11-27 | Preprint
DOI: 10.31219/osf.io/am5ck
Contributors: Simon Schwab; Perrine Janiaud; Michael Dayan; Valentin Amrhein; Radoslaw Panczak; Patricia M. Palagi; Lars G. Hemkens; Meike Ramon; Nicolas Rothen; Stephen Senn et al.
Source: check_circle
Crossref

Making training materials FAIR experiences, challenges, solutions

ISMB ECCB 2021
2021-07-25 | Conference abstract
DOI: https://doi.org/10.5281/zenodo.5820221
Source: Self-asserted source
Patricia M. Palagi

Open and FAIR in bioinformatics and training

Open Science Zurich
2021-03-04 | Conference abstract
DOI: 10.5281/zenodo.4581176
Source: Self-asserted source
Patricia M. Palagi

Biocuration - mapping resources and needs [version 2; peer review: 2 approved]

2020-12-02 | Journal article
DOI: 10.12688/f1000research.25413.2
Part of ISSN: 2046-1402
Contributors: Alexandra Holinski; Melissa L. Burke; Sarah L. Morgan; Peter McQuilton; Patricia M. Palagi
Source: check_circle
F1000
grade
Preferred source (of 2)‎

Course design: Considerations for trainers – a Professional Guide

F1000Research
2020-11-27 | Manual
DOI: 10.7490/F1000RESEARCH.1118395.1
Contributors: Patricia M. Palagi
Source: Self-asserted source
Patricia M. Palagi

Lessons learned when moving SIB Training courses from in-person to online – anything in bioinformatics can be taught online, but not anyhow

F1000Research
2020-09-17 | Research protocol or technique
DOI: 10.7490/F1000RESEARCH.1118316.1
Source: Self-asserted source
Patricia M. Palagi

Biocuration - mapping resources and needs

F1000Research
2020-09-04 | Journal article
DOI: 10.12688/f1000research.25413.1
Contributors: Alexandra Holinski; Melissa L. Burke; Sarah L. Morgan; Peter McQuilton; Patricia M. Palagi
Source: check_circle
Crossref

Clinical bioinformatics for microbial genomics and metagenomics: an ESCMID Postgraduate Technical Workshop

Microbes and Infection
2020-08 | Journal article
DOI: 10.1016/j.micinf.2020.07.008
Part of ISSN: 1286-4579
Source: Self-asserted source
Patricia M. Palagi

A framework to assess the quality and impact of bioinformatics training across ELIXIR.

PLoS computational biology
2020-07 | Journal article
DOI: 10.1371/journal.pcbi.1007976
PMID: 32702016
PMC: PMC7377377
Contributors: Gurwitz KT; Singh Gaur P; Bellis LJ; Larcombe L; Alloza E; Balint BL; Botzki A; Dimec J; Dominguez Del Angel V; Fernandes PL et al.
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

Ten simple rules for making training materials FAIR

PLOS Computational Biology
2020-05 | Journal article
DOI: 10.1371/journal.pcbi.1007854
Part of ISSN: 1553-7358
Contributors: Leyla Garcia; Bérénice Batut; Melissa L. Burke; Mateusz Kuzak; Fotis Psomopoulos; Ricardo Arcila; Teresa K. Attwood; Niall Beard; Denise Carvalho-Silva; Alexandros C. Dimopoulos et al.
Source: Self-asserted source
Patricia M. Palagi via Crossref Metadata Search

Bioinformatics on a national scale: an example from Switzerland.

Briefings in bioinformatics
2019-03 | Journal article
DOI: 10.1093/bib/bbx073
PMID: 29106442
PMC: PMC6433736
Contributors: Baillie Gerritsen V; Palagi PM; Durinx C
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action.

F1000Research
2017 | Journal article
DOI: 10.12688/f1000research.11718.1
PMID: 28781745
PMC: PMC5516217
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

A new pan-European Train-the-Trainer programme for bioinformatics: pilot results on feasibility, utility and sustainability of learning

Briefings in Bioinformatics
2017-09 | Journal article
DOI: 10.1093/bib/bbx112
Part of ISSN: 1477-4054
Contributors: Allegra Via; Teresa K Attwood; Pedro L Fernandes; Sarah L Morgan; Maria Victoria Schneider; Patricia M Palagi; Gabriella Rustici; Rochelle E Tractenberg
Source: Self-asserted source
Patricia M. Palagi via Crossref Metadata Search

BioCIDER: a Contextualisation InDEx for biological Resources discovery.

Bioinformatics (Oxford, England)
2017-08 | Journal article
DOI: 10.1093/bioinformatics/btx213
PMID: 28407033
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training

F1000Research
2017-08-24 | Journal article
DOI: 10.12688/f1000research.12332.1
Contributors: Sarah L Morgan; Patricia M Palagi; Pedro L Fernandes; Eija Koperlainen; Jure Dimec; Diana Marek; Lee Larcombe; Gabriella Rustici; Teresa K Attwood; Allegra Via
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

Nucleic acids research
2016-01 | Journal article
DOI: 10.1093/nar/gkv1310
PMID: 26615188
PMC: PMC4702916
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

Correction: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training.

2015-05 | Journal article
DOI: 10.1371/journal.pcbi.1004281
PMID: 25974841
PMC: PMC4431671
Contributors: Attwood TK; Bongcam-Rudloff E; Brazas ME; Corpas M; Gaudet P; Lewitter F; Mulder N; Palagi PM; Schneider MV; van Gelder CW et al.
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training.

2015-04 | Journal article
DOI: 10.1371/journal.pcbi.1004143
PMID: 25856076
PMC: PMC4391932
Contributors: Attwood TK; Bongcam-Rudloff E; Brazas ME; Corpas M; Gaudet P; Lewitter F; Mulder N; Palagi PM; Schneider MV; van Gelder CW et al.
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers.

2015-01 | Journal article
DOI: 10.1093/bioinformatics/btu601
PMID: 25189782
PMC: PMC4271145
Contributors: Corpas M; Jimenez RC; Bongcam-Rudloff E; Budd A; Brazas MD; Fernandes PL; Gaeta B; van Gelder C; Korpelainen E; Lewitter F et al.
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

Differential accumulation of soluble proteins in roots of metallicolous and nonmetallicolous populations of Agrostis capillaris L. exposed to Cu.

2014-08 | Journal article
DOI: 10.1002/pmic.201300168
PMID: 24842164
Contributors: Hego E; Bes CM; Bedon F; Palagi PM; Chaumeil P; Barré A; Claverol S; Dupuy JW; Bonneu M; Lalanne C et al.
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

2014-07 | Journal article
DOI: 10.1093/nar/gku380
PMID: 24792157
PMC: PMC4086091
Contributors: Stockinger H; Altenhoff AM; Arnold K; Bairoch A; Bastian F; Bergmann S; Bougueleret L; Bucher P; Delorenzi M; Lane L et al.
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

A quick guide to genomics and bioinformatics training for clinical and public audiences.

2014-04 | Journal article
DOI: 10.1371/journal.pcbi.1003510
PMID: 24722068
PMC: PMC3983038
Contributors: Brazas MD; Lewitter F; Schneider MV; van Gelder CW; Palagi PM
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

Calmodulin expression distinguishes the smooth muscle cell population of human carotid plaque.

2013-09 | Journal article
DOI: 10.1016/j.ajpath.2013.06.006
PMID: 23838429
Contributors: Coen M; Marchetti G; Palagi PM; Zerbinati C; Guastella G; Gagliano T; Bernardi F; Mascoli F; Bochaton-Piallat ML
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

LC/MS data processing for label-free quantitative analysis.

2011 | Journal article
DOI: 10.1007/978-1-60761-987-1_24
PMID: 21063961
Contributors: Palagi PM; Müller M; Walther D; Lisacek F
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

Database interrogation algorithms for identification of proteins in proteomic separations.

2009 | Journal article
DOI: 10.1007/978-1-59745-281-6_35
PMID: 19381607
Contributors: Palagi PM; Lisacek F; Appel RD
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

A suite of tools to analyse and publish 2-DE data.

2008-12 | Journal article
DOI: 10.1002/pmic.200800301
PMID: 19072735
Contributors: Hoogland C; Walther D; Palagi PM; Bouchet G; Mostaguir K; Robin X; Appel RD; Lisacek F
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central

The Swiss Proteomics Society (SPS) was one of the first European associations to be created in the field of proteomics.

2008-07 | Journal article
DOI: 10.1016/j.jprot.2008.06.001
PMID: 18572009
Contributors: Palagi PM; Sanchez JC
Source: Self-asserted source
Patricia M. Palagi via Europe PubMed Central
Items per page:
Page 1 of 2

Peer review (2 reviews for 2 publications/grants)

Review activity for F1000Research. (1)
Review activity for PLoS computational biology. (1)
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