Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.

Janne Lehtiö

Husen M. Umer Enrique Audain Yafeng Zhu Julianus Pfeuffer Timo Sachsenberg Janne Lehtiö Rui Mamede Branca Yasset Pérez-Riverol Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides. 1470-1472 2022 38 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btab838 db/journals/bioinformatics/bioinformatics38.html#UmerAZPSLBP22

Ilona Kifer Rui Mamede Branca Amir Ben-Dor Linhui Zhai Ping Xu Janne Lehtiö Zohar Yakhini Optimizing Analytical Depth and Cost Efficiency of IEF-LC/MS Proteomics. 272-281 2017 14 IEEE ACM Trans. Comput. Biol. Bioinform. 2 https://doi.org/10.1109/TCBB.2015.2452901 https://doi.ieeecomputersociety.org/10.1109/TCBB.2015.2452901 https://dl.acm.org/doi/10.1109/TCBB.2015.2452901 https://www.wikidata.org/entity/Q38860776 db/journals/tcbb/tcbb14.html#KiferBBZXLY17

Ilona Kifer Amir Ben-Dor Zohar Yakhini Rui Mamede Branca Janne Lehtiö Ping Xu Optimizing analytical depth and cost efficiency of IEF-LC/MS proteomics. 99-106 2014 BIBM https://doi.org/10.1109/BIBM.2014.6999136 https://doi.ieeecomputersociety.org/10.1109/BIBM.2014.6999136 conf/bibm/2014 db/conf/bibm/bibm2014.html#KiferBYBLX14

Andrey Alexeyenko Woojoo Lee Maria Pernemalm Justin Guegan Philippe Dessen Vladimir Lazar Janne Lehtiö Yudi Pawitan Network enrichment analysis: extension of gene-set enrichment analysis to gene networks. 226 2012 13 BMC Bioinform. https://doi.org/10.1186/1471-2105-13-226 https://www.wikidata.org/entity/Q34411128 db/journals/bmcbi/bmcbi13.html#AlexeyenkoLPGDLLP12

Lina Hultin Rosenberg Bo Franzén Gert Auer Janne Lehtiö Jenny Forshed Multivariate meta-analysis of proteomics data from human prostate and colon tumours. 468 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-468 https://www.wikidata.org/entity/Q33694799 db/journals/bmcbi/bmcbi11.html#RosenbergFALF10

Chuen Seng Tan Agus Salim Alexander Ploner Janne Lehtiö Kee Seng Chia Yudi Pawitan Correlating gene and protein expression data using Correlated Factor Analysis. 272 2009 10 BMC Bioinform. https://doi.org/10.1186/1471-2105-10-272 https://www.wikidata.org/entity/Q33499086 db/journals/bmcbi/bmcbi10.html#TanSPLCP09

Chuen Seng Tan Alexander Ploner Andreas Quandt Janne Lehtiö Yudi Pawitan Finding regions of significance in SELDI measurements for identifying protein biomarkers. 1515-1523 2006 22 Bioinform. 12 https://doi.org/10.1093/bioinformatics/btl106 https://www.wikidata.org/entity/Q33237787 db/journals/bioinformatics/bioinformatics22.html#TanPQLP06

Andreas Quandt Alexander Ploner Chuen Seng Tan Janne Lehtiö Yudi Pawitan ProSpect: An R Package for Analyzing SELDI Measurements Identifying Protein Biomarkers. 140-150 2005 conf/complife/2005 CompLife https://doi.org/10.1007/11560500_13 db/conf/complife/complife2005.html#QuandtPTLP05 Andrey Alexeyenko Enrique Audain Gert Auer Amir Ben-Dor Rui Mamede Branca Kee Seng Chia Philippe Dessen Jenny Forshed Bo Franzén Justin Guegan Ilona Kifer Vladimir Lazar Woojoo Lee Yudi Pawitan Yasset Pérez-Riverol Maria Pernemalm Julianus Pfeuffer Alexander Ploner Andreas Quandt Lina Hultin Rosenberg Timo Sachsenberg Agus Salim Chuen Seng Tan Husen M. Umer Ping Xu Zohar Yakhini Linhui Zhai Yafeng Zhu