Works by Vaudel, Marc

Results: 42

BioContainers: an open-source and community-driven framework for software standardization.

Published in:

Bioinformatics, 2017, v. 33, n. 16, p. 2580, doi. 10.1093/bioinformatics/btx192

By:

Leprevost, Felipe da Veiga;
Grüning, Björn A.;
Aflitos, Saulo Alves;
Röst, Hannes L.;
Uszkoreit, Julian;
Barsnes, Harald;
Vaudel, Marc;
Moreno, Pablo;
Gatto, Laurent;
Weber, Jonas;
Mingze Bai;
Jimenez, Rafael C.;
Sachsenberg, Timo;
Pfeuffer, Julianus;
Alvarez, Roberto Vera;
Griss, Johannes;
Nesvizhskii, Alexey I.;
Perez-Riverol, Yasset

Publication type:

Article

PeptideMapper: efficient and versatile amino acid sequence and tag mapping.

Published in:

Bioinformatics, 2017, v. 33, n. 13, p. 2042, doi. 10.1093/bioinformatics/btx122

By:

Kopczynski, Dominik;
Barsnes, Harald;
Njølstad, Pål R.;
Sickmann, Albert;
Vaudel, Marc;
Ahrends, Robert

Publication type:

Article

Reliable FASP-based procedures for optimal quantitative proteomic and phosphoproteomic analysis on samples from acute myeloid leukemia patients.

Published in:

Biological Procedures Online, 2016, v. 18, p. 1, doi. 10.1186/s12575-016-0043-0

By:

Hernandez-Valladares, Maria;
Aasebø, Elise;
Mjaavatten, Olav;
Vaudel, Marc;
Bruserud, Øystein;
Berven, Frode;
Selheim, Frode

Publication type:

Article

Anatomy and evolution of database search engines—a central component of mass spectrometry based proteomic workflows.

Published in:

Mass Spectrometry Reviews, 2020, v. 39, n. 3, p. 292, doi. 10.1002/mas.21543

By:

Verheggen, Kenneth;
Ræder, Helge;
Berven, Frode S.;
Martens, Lennart;
Barsnes, Harald;
Vaudel, Marc

Publication type:

Article

Rare copy number variation in autoimmune Addison's disease.

Published in:

Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2024.1374499

By:

Artaza, Haydee;
Eriksson, Daniel;
Lavrichenko, Ksenia;
Aranda-Guillén, Maribel;
Bratland, Eirik;
Vaudel, Marc;
Knappskog, Per;
Husebye, Eystein S.;
Bensing, Sophie;
Wolff, Anette S. B.;
Kämpe, Olle;
Røyrvik, Ellen C.;
Johansson, Stefan

Publication type:

Article

A proteomics sample metadata representation for multiomics integration and big data analysis.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26111-3

By:

Dai, Chengxin;
Füllgrabe, Anja;
Pfeuffer, Julianus;
Solovyeva, Elizaveta M.;
Deng, Jingwen;
Moreno, Pablo;
Kamatchinathan, Selvakumar;
Kundu, Deepti Jaiswal;
George, Nancy;
Fexova, Silvie;
Grüning, Björn;
Föll, Melanie Christine;
Griss, Johannes;
Vaudel, Marc;
Audain, Enrique;
Locard-Paulet, Marie;
Turewicz, Michael;
Eisenacher, Martin;
Uszkoreit, Julian;
Van Den Bossche, Tim

Publication type:

Article

Exploring the Human Plasma Proteome for Humoral Mediators of Remote Ischemic Preconditioning - A Word of Caution.

Published in:

PLoS ONE, 2014, v. 9, n. 10, p. 1, doi. 10.1371/journal.pone.0109279

By:

Helgeland, Erik;
Breivik, Lars Ertesvåg;
Vaudel, Marc;
Svendsen, Øyvind Sverre;
Garberg, Hilde;
Nordrehaug, Jan Erik;
Berven, Frode Steingrimsen;
Jonassen, Anne Kristine

Publication type:

Article

Rare copy number variant analysis in case–control studies using snp array data: a scalable and automated data analysis pipeline.

Published in:

BMC Bioinformatics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12859-024-05979-0

By:

Artaza, Haydee;
Lavrichenko, Ksenia;
Wolff, Anette S. B.;
Røyrvik, Ellen C.;
Vaudel, Marc;
Johansson, Stefan

Publication type:

Article

Autozygosity mapping and time-to-spontaneous delivery in Norwegian parent-offspring trios.

Published in:

Human Molecular Genetics, 2020, v. 29, n. 23, p. 3845, doi. 10.1093/hmg/ddaa255

By:

Sole-Navais, Pol;
Bacelis, Jonas;
Helgeland, Øyvind;
Modzelewska, Dominika;
Vaudel, Marc;
Flatley, Christopher;
Andreassen, Ole;
Njølstad, Pål R;
Muglia, Louis J;
Johansson, Stefan;
Zhang, Ge;
Jacobsson, Bo

Publication type:

Article

Automated splitting into batches for observational biomedical studies with sequential processing.

Published in:

Biostatistics, 2023, v. 24, n. 4, p. 1031, doi. 10.1093/biostatistics/kxac014

By:

Burger, Bram;
Vaudel, Marc;
Barsnes, Harald

Publication type:

Article

GWAS for autoimmune Addison's disease identifies multiple risk loci and highlights AIRE in disease susceptibility.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-21015-8

By:

Eriksson, Daniel;
Røyrvik, Ellen Christine;
Aranda-Guillén, Maribel;
Berger, Amund Holte;
Landegren, Nils;
Artaza, Haydee;
Hallgren, Åsa;
Grytaas, Marianne Aardal;
Ström, Sara;
Bratland, Eirik;
Botusan, Ileana Ruxandra;
Oftedal, Bergithe Eikeland;
Breivik, Lars;
Vaudel, Marc;
Helgeland, Øyvind;
Falorni, Alberto;
Jørgensen, Anders Palmstrøm;
Hulting, Anna-Lena;
Svartberg, Johan;
Ekwall, Olov

Publication type:

Article

Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia.

Published in:

Cancers, 2020, v. 12, n. 3, p. 709, doi. 10.3390/cancers12030709

By:

Aasebø, Elise;
Berven, Frode S.;
Bartaula-Brevik, Sushma;
Stokowy, Tomasz;
Hovland, Randi;
Vaudel, Marc;
Døskeland, Stein Ove;
McCormack, Emmet;
Batth, Tanveer S.;
Olsen, Jesper V.;
Bruserud, Øystein;
Selheim, Frode;
Hernandez-Valladares, Maria

Publication type:

Article

Reprogrammed Cells Display Distinct Proteomic Signatures Associated with Colony Morphology Variability.

Published in:

Stem Cells International, 2019, p. 1, doi. 10.1155/2019/8036035

By:

Bjørlykke, Yngvild;
Søviknes, Anne M.;
Hoareau, Laurence;
Vethe, Heidrun;
Mathisen, Andreas F.;
Chera, Simona;
Vaudel, Marc;
Ghila, Luiza M.;
Ræder, Helge

Publication type:

Article

Bioinformatics pipeline for the systematic mining genomic and proteomic variation linked to rare diseases: The example of monogenic diabetes.

Published in:

PLoS ONE, 2024, v. 19, n. 4, p. 1, doi. 10.1371/journal.pone.0300350

By:

Kuznetsova, Ksenia G.;
Vašíček, Jakub;
Skiadopoulou, Dafni;
Molnes, Janne;
Udler, Miriam;
Johansson, Stefan;
Njølstad, Pål Rasmus;
Manning, Alisa;
Vaudel, Marc

Publication type:

Article

Smoking during pregnancy and its effect on placental weight: a Mendelian randomization study.

Published in:

BMC Pregnancy & Childbirth, 2024, v. 24, n. 1, p. 1, doi. 10.1186/s12884-024-06431-0

By:

Jaitner, Annika;
Vaudel, Marc;
Tsaneva-Atanasova, Krasimira;
Njølstad, Pål R.;
Jacobsson, Bo;
Bowden, Jack;
Johansson, Stefan;
Freathy, Rachel M.

Publication type:

Article

Genome-wide analyses of neonatal jaundice reveal a marked departure from adult bilirubin metabolism.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-51947-w

By:

Solé-Navais, Pol;
Juodakis, Julius;
Ytterberg, Karin;
Wu, Xiaoping;
Bradfield, Jonathan P.;
Vaudel, Marc;
LaBella, Abigail L.;
Helgeland, Øyvind;
Flatley, Christopher;
Geller, Frank;
Finel, Moshe;
Zhao, Mengqi;
Lazarus, Philip;
Hakonarson, Hakon;
Magnus, Per;
Andreassen, Ole A.;
Njølstad, Pål R.;
Grant, Struan F. A.;
Feenstra, Bjarke;
Muglia, Louis J.

Publication type:

Article

A Potential Golden Age to Come—Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics.

Published in:

Proteomics, 2018, v. 18, n. 18, p. 1, doi. 10.1002/pmic.201700150

By:

Muth, Thilo;
Hartkopf, Felix;
Vaudel, Marc;
Renard, Bernhard Y.

Publication type:

Article

Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis.

Published in:

Proteomics, 2016, v. 16, n. 7, p. 1154, doi. 10.1002/pmic.201500284

By:

Opsahl, Jill A.;
Vaudel, Marc;
Guldbrandsen, Astrid;
Aasebø, Elise;
Pesch, Vincent;
Franciotta, Diego;
Myhr, Kjell‐Morten;
Barsnes, Harald;
Berle, Magnus;
Torkildsen, Øivind;
Kroksveen, Ann C.;
Berven, Frode S.

Publication type:

Article

Exploring the potential of public proteomics data.

Published in:

Proteomics, 2016, v. 16, n. 2, p. 214, doi. 10.1002/pmic.201500295

By:

Vaudel, Marc;
Verheggen, Kenneth;
Csordas, Attila;
Ræder, Helge;
Berven, Frode S.;
Martens, Lennart;
Vizcaíno, Juan A.;
Barsnes, Harald

Publication type:

Article

JSparklines: Making tabular proteomics data come alive.

Published in:

Proteomics, 2015, v. 15, n. 8, p. 1428, doi. 10.1002/pmic.201400356

By:

Barsnes, Harald;
Vaudel, Marc;
Martens, Lennart

Publication type:

Article

Performance of super-SILAC based quantitative proteomics for comparison of different acute myeloid leukemia (AML) cell lines.

Published in:

Proteomics, 2014, v. 14, n. 17/18, p. 1971, doi. 10.1002/pmic.201300448

By:

Aasebø, Elise;
Vaudel, Marc;
Mjaavatten, Olav;
Gausdal, Gro;
Burgh, Arthur;
Gjertsen, Bjørn Tore;
Døskeland, Stein Ove;
Bruserud, Øystein;
Berven, Frode S.;
Selheim, Frode

Publication type:

Article

Shedding light on black boxes in protein identification.

Published in:

Proteomics, 2014, v. 14, n. 9, p. 1001, doi. 10.1002/pmic.201300488

By:

Vaudel, Marc;
Venne, A. Saskia;
Berven, Frode S.;
Zahedi, René P.;
Martens, Lennart;
Barsnes, Harald

Publication type:

Article

D-score: A search engine independent MD-score.

Published in:

Proteomics, 2013, v. 13, n. 6, p. 1036, doi. 10.1002/pmic.201200408

By:

Vaudel, Marc;
Breiter, Daniela;
Beck, Florian;
Rahnenführer, Jörg;
Martens, Lennart;
Zahedi, René P.

Publication type:

Article

Peptide identification quality control.

Published in:

Proteomics, 2011, v. 11, n. 10, p. 2105, doi. 10.1002/pmic.201000704

By:

Vaudel, Marc;
Burkhart, Julia M.;
Sickmann, Albert;
Martens, Lennart;
Zahedi, René P.

Publication type:

Article

iTRAQ protein quantification: A quality-controlled workflow.

Published in:

Proteomics, 2011, v. 11, n. 6, p. 1125, doi. 10.1002/pmic.201000711

By:

Burkhart, Julia M.;
Vaudel, Marc;
Zahedi, René P.;
Martens, Lennart;
Sickmann, Albert

Publication type:

Article

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

Published in:

Proteomics, 2011, v. 11, n. 5, p. 996, doi. 10.1002/pmic.201000595

By:

Vaudel, Marc;
Barsnes, Harald;
Berven, Frode S.;
Sickmann, Albert;
Martens, Lennart

Publication type:

Article

Erratum: XTandem Parser: An open-source library to parse and analyse X!Tandem MS/MS search results.

Published in:

Proteomics, 2010, v. 10, n. 13, p. 2560, doi. 10.1002/pmic.201090058

By:

Muth, Thilo;
Vaudel, Marc;
Barsnes, Harald;
Martens, Lennart;
Sickmann, Albert

Publication type:

Article

XTandem Parser: An open-source library to parse and analyse X!Tandem MS/MS search results.

Published in:

Proteomics, 2010, v. 10, n. 7, p. 1522, doi. 10.1002/pmic.200900759

By:

Muth, Thilo;
Vaudel, Marc;
Barsnes, Harald;
Martens, Lennart;
Sickmann, Albert

Publication type:

Article

Peptide and protein quantification: A map of the minefield.

Published in:

Proteomics, 2010, v. 10, n. 4, p. 650, doi. 10.1002/pmic.200900481

By:

Vaudel, Marc;
Sickmann, Albert;
Martens, Lennart

Publication type:

Article

Genome-wide association study reveals dynamic role of genetic variation in infant and early childhood growth.

Published in:

Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-12308-0

By:

Helgeland, Øyvind;
Vaudel, Marc;
Juliusson, Petur B.;
Lingaas Holmen, Oddgeir;
Juodakis, Julius;
Bacelis, Jonas;
Jacobsson, Bo;
Lindekleiv, Haakon;
Hveem, Kristian;
Lie, Rolv Terje;
Knudsen, Gun Peggy;
Stoltenberg, Camilla;
Magnus, Per;
Sagen, Jørn V.;
Molven, Anders;
Johansson, Stefan;
Njølstad, Pål Rasmus

Publication type:

Article

Introducing M-GCTA a Software Package to Estimate Maternal (or Paternal) Genetic Effects on Offspring Phenotypes.

Published in:

Behavior Genetics, 2020, v. 50, n. 1, p. 51, doi. 10.1007/s10519-019-09969-4

By:

Qiao, Zhen;
Zheng, Jie;
Helgeland, Øyvind;
Vaudel, Marc;
Johansson, Stefan;
Njølstad, Pål R.;
Smith, George Davey;
Warrington, Nicole M.;
Evans, David M.

Publication type:

Article

Spatial Environment Affects HNF4A Mutation-Specific Proteome Signatures and Cellular Morphology in hiPSC-Derived β-Like Cells.

Published in:

2022

By:

Carrasco, Manuel;
Wang, Chencheng;
Søviknes, Anne M.;
Bjørlykke, Yngvild;
Abadpour, Shadab;
Paulo, Joao A.;
Tjora, Erling;
Njølstad, Pål;
Ghabayen, Jonas;
Nermoen, Ingrid;
Lyssenko, Valeriya;
Chera, Simona;
Ghila, Luiza M.;
Vaudel, Marc;
Scholz, Hanne;
Ræder, Helge

Publication type:

journal article

compomics-utilities: an open-source Java library for computational proteomics.

Published in:

BMC Bioinformatics, 2011, v. 12, n. 1, p. 70, doi. 10.1186/1471-2105-12-70

By:

Barsnes, Harald;
Vaudel, Marc;
Colaert, Niklaas;
Helsens, Kenny;
Sickmann, Albert;
Berven, Frode S.;
Martens, Lennart

Publication type:

Article

Extending protein interaction networks using proteoforms and small molecules.

Published in:

Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad598

By:

Sánchez, Luis Francisco Hernández;
Burger, Bram;
Campos, Rodrigo Alexander Castro;
Johansson, Stefan;
Njølstad, Pål Rasmus;
Barsnes, Harald;
Vaudel, Marc

Publication type:

Article

PDV: an integrative proteomics data viewer.

Published in:

Bioinformatics, 2019, v. 35, n. 7, p. 1249, doi. 10.1093/bioinformatics/bty770

By:

Li, Kai;
Ren, Yan;
Vaudel, Marc;
Zhang, Bing;
Wen, Bo

Publication type:

Article

Finding haplotypic signatures in proteins.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad093

By:

Vašíček, Jakub;
Skiadopoulou, Dafni;
Kuznetsova, Ksenia G;
Wen, Bo;
Johansson, Stefan;
Njølstad, Pål R;
Bruckner, Stefan;
Käll, Lukas;
Vaudel, Marc

Publication type:

Article

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping.

Published in:

GigaScience, 2019, v. 8, n. 8, p. N.PAG, doi. 10.1093/gigascience/giz088

By:

Sánchez, Luis Francisco Hernández;
Burger, Bram;
Horro, Carlos;
Fabregat, Antonio;
Johansson, Stefan;
Njølstad, Pål Rasmus;
Barsnes, Harald;
Hermjakob, Henning;
Vaudel, Marc

Publication type:

Article

Software engineering for scientific big data analysis.

Published in:

GigaScience, 2019, v. 8, n. 5, p. N.PAG, doi. 10.1093/gigascience/giz054

By:

Grüning, Björn A;
Lampa, Samuel;
Vaudel, Marc;
Blankenberg, Daniel

Publication type:

Article

Dynamic proteome profiling of human pluripotent stem cell‐derived pancreatic progenitors.

Published in:

Stem Cells, 2020, v. 38, n. 4, p. 542, doi. 10.1002/stem.3135

By:

Loo, Larry Sai Weng;
Vethe, Heidrun;
Soetedjo, Andreas Alvin Purnomo;
Paulo, Joao A.;
Jasmen, Joanita;
Jackson, Nicholas;
Bjørlykke, Yngvild;
Valdez, Ivan A.;
Vaudel, Marc;
Barsnes, Harald;
Gygi, Steven P.;
Ræder, Helge;
Teo, Adrian Kee Keong;
Kulkarni, Rohit N.

Publication type:

Article

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

Published in:

Nature Biotechnology, 2015, v. 33, n. 1, p. 22, doi. 10.1038/nbt.3109

By:

Vaudel, Marc;
Burkhart, Julia M;
Zahedi, René P;
Oveland, Eystein;
Berven, Frode S;
Sickmann, Albert;
Martens, Lennart;
Barsnes, Harald

Publication type:

Article

Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers.

Published in:

Expert Review of Proteomics, 2017, v. 14, n. 8, p. 649, doi. 10.1080/14789450.2017.1352474

By:

Hernandez-Valladares, Maria;
Vaudel, Marc;
Selheim, Frode;
Berven, Frode;
Bruserud, Øystein

Publication type:

Article

Current methods for global proteome identification.

Published in:

Expert Review of Proteomics, 2012, v. 9, n. 5, p. 519, doi. 10.1586/EPR.12.51

By:

Vaudel, Marc;
Sickmann, Albert;
Martens, Lennart

Publication type:

Article