P
Pieter Lukasse
Researcher at Wageningen University and Research Centre
Publications - 7
Citations - 203
Pieter Lukasse is an academic researcher from Wageningen University and Research Centre. The author has contributed to research in topics: Peptide & Proteomics Standards Initiative. The author has an hindex of 4, co-authored 6 publications receiving 159 citations. Previous affiliations of Pieter Lukasse include Netherlands Bioinformatics Centre.
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Journal ArticleDOI
Multi-omic data analysis using Galaxy
Jorrit Boekel,John Chilton,Ira Cooke,Peter Horvatovich,Pratik D. Jagtap,Lukas Käll,Janne Lehtiö,Pieter Lukasse,Perry D. Moerland,Timothy J. Griffin +9 more
TL;DR: Galaxy 8 can be used as one solution to the problem of integrated analysis of raw multi-omic data, demanding the use of disparate software programs and requiring computational resources beyond the capacity of most biological research laboratories.
Journal ArticleDOI
Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML
Fawaz Ghali,Ritesh Krishna,Pieter Lukasse,Pieter Lukasse,Salvador Martínez-Bartolomé,Florian Reisinger,Henning Hermjakob,Juan Antonio Vizcaíno,Andrew R. Jones +8 more
TL;DR: Several open-source Java-based software packages based on mzIdentML are reported, anticipating that these developments will simplify adoption of the new standard in proteomics laboratories and the integration of mZIdentML into other software tools.
Proceedings ArticleDOI
Abstract 5277: The cBioPortal for cancer genomics and its application in precision oncology
Jianjiong Gao,James Lindsay,Stuart Watt,Istemi Bahceci,Pieter Lukasse,Adam Abeshouse,Hsiao-Wei Chen,Ino de Bruijn,Benjamin Gross,Dong Li,Ritika Kundra,Zachary J. Heins,Jorge S. Reis-Filho,Onur Sumer,Yichao Sun,Jiaojiao Wang,Qingguo Wang,Hongxin Zhang,Priti Kumari,M. Furkan Sahin,Sander de Ridder,Fedde Schaeffer,Kees van Bochove,Ugur Dogrusoz,Trevor J. Pugh,Chris Sander,Ethan Cerami,Nikolaus Schultz +27 more
TL;DR: The cBioPortal for cancer genomics software has the potential to facilitate the use of genomic data in clinical decision making, and as the sequencing of tumor samples has entered clinical practice, the features are expanding so that it can be used for precision medicine at cancer centers.
Journal ArticleDOI
Protein Inference Using Peptide Quantification Patterns
TL;DR: The basis for a new way of performing protein inference based on accurate quantification patterns of identified peptides using the correlation of these patterns to validate peptide to protein matches is introduced.
Proceedings ArticleDOI
Abstract 923: The cBioPortal for Cancer Genomics: An intuitive open-source platform for exploration, analysis and visualization of cancer genomics data
Jianjiong Gao,Tali Mazor,Ersin Ciftci,Pichai Raman,Pieter Lukasse,Istemi Bahceci,Alexandros Sigaras,Adam Abeshouse,Ino de Bruijn,Benjamin Gross,Ritika Kundra,Aaron Lisman,Angelica Ochoa,Robert L. Sheridan,Jing Su,Selcuk Onur Sumer,Yichao Sun,Avery Wang,Jiaojiao Wang,Manda Wilson,Hongxin Zhang,Priti Kumari,James Lindsay,Karthik Kalletla,Kelsey Zhu,Oleguer Plantalech,Fedde Schaeffer,Sander Tan,Dionne Zaal,Sjoerd van Hagen,Kees van Bochove,Ugur Dogrusoz,Trevor J. Pugh,Adam C. Resnick,Chris Sander,Nikolaus Schultz,Ethan Cerami +36 more
TL;DR: The cBioPortal for Cancer Genomics is an open source software platform that enables interactive, exploratory analysis of large-scale cancer genomics data sets, and provides a suite of visualization and analysis options, including cohort and patient-level visualization, mutation visualization, survival analysis, alteration enrichment analysis, and network analysis.