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Publications

Marc Vaudel 2019-08-01

with the submission This repository lists the scientific publications co-authored by Marc Vaudel as of 25.08.2024.


1 shared first, $ correspondence, † shared last.


Ten highlighted recent publications

  1. Vašíček J, Kuznetsova KG, Skiadopoulou D, Njølstad PR, Johansson S, Bruckner S†, Käll L†, Vaudel M†,$. ProHap enables proteomic database generation accounting for population diversity, preprint. [Preprint]

ProHap

ProHap enables the creation of protein sequence databases from reference phased haplotypes. The tool can be used on public or private reference panels to build protein sequence databases that reflect the sequence diversity of a study population. Along with the tool, we provide protein sequences derived from the common haplotypes of the thousand genomes redily usable for proteomic studies: doi 10.5281/zenodo.10149278.


  1. Kuznetsova KG$, Vašíček J, Skiadopoulou D, Molnes J, Udler M, Johansson S, Njølstad PR, Manning A†, Vaudel M†,$. A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes, Plos One, 2024. [PubMed id 38635808] [doi: 10.1371/journal.pone.0300350] [pdf]

Sequence generation pipeline

A pipeline that maps, curates, and consolidates the variants associated with monogenic diabetes and translate their consequences to the protein level onto common haplotypes. We use this pipeline to design custom proteomics database and mine for variant peptides in the Norwegian diabetes registries. The pipeline can be used for other diseases.


  1. Jaitner A, Vaudel M, Tsaneva-Atanasova K, Njølstad PR, Jacobsson B, Bowden J, Johansson S, Freathy R$. Smoking during pregnancy and its effect on placental weight: A Mendelian randomization study, BMC Pregnancy Childbirth, 2024. [PubMed id 38575863] [doi: 10.1186/s12884-024-06431-0] [pdf]

MR Placental Weight

The relationship between smoking and placental weight is controversial, studies inconsistently report smaller and larger placentae for smokers. We conducted a Mendelian randomization among pre-pregnancy smokers of the ALSPAC and MoBa studies. Our results show that continuous smoking during pregancy causes a higher placental weight and in turn suggest a lower birth weight relative to the placental weight, possibly indicating a malfunction of the placenta for these pregnancies.


  1. Skiadopoulou D, Vašíček J, Kuznetsova KG, Käll L†, Vaudel M†,$. Retention time and fragmentation predictors increase confidence in variant peptide identification, Journal of Proteome Research, 2023. [PubMed id 37656829] [doi: 10.1021/acs.jproteome.3c00243] [pdf]

Predictors performance

We demonstrate that common variation can be included without affecting the identification rate. We further show how retention time and fragmentation predictors can be used to help the machine learning-based Percolator distinguish variant peptides from similar, possibly modified, peptides.


  1. Vašíček J1, Skiadopoulou D1, Kuznetsova KG, Wen B, Johansson S, Njølstad PR, Bruckner S, Käll L†, Vaudel M†,$. Finding Haplotypic Signatures in Proteins, Gigascience, 2023. [PubMed id 37919975] [doi: 10.1093/gigascience/giad093] [pdf]

Protein Haplotypes

A study of the distribution of protein haplotypes, and whether they can be identified by mass spectrometry. We show the prevalence of muli-variant peptides that can be identified, and how these are difficult to distinguish from similar peptides carrying PTMs.


  1. Beaumont RN1, Flatley C1, Vaudel M1, Xiaoping W, Chen J, Moen GH, Skotte L, Helgeland Ø, Sole-Navais P, Banasik K, Albiñana C, Ronkainen J, Fadista J, Stinson SE, Trajanoska K, Wang CA, Westergaard D, Srinivasan S, Sánchez-Soriano C, Bilbao JR, Allard C, Groleau M, Kuulasmaa T, Leirer DJ, White F, Jacques PE, Cheng H, Hao K, Andreassen OA, Åsvold BO, Atalay M, Bhatta L, Bouchard L, Brumpton BM, Brunak S, Bybjerg-Grauholm J, Ebbing C, Elliott P, Engelbrechtsen L, Erikstrup C, Estarlich M, Franks S, Gaillard R, Geller F, Grove J, Hougaard DM, Kajantie E, Morgen CS, Nohr EA, Nyegaard M, Palmer CNA, Pedersen OB, The Early Growth Genetics (EGG) Consortium, Rivadeneira F, Sebert S, Shields BM, Stoltenberg C, Surakka I, Thørner LW, Ullum H, Vaarasmaki M, Vilhjalmsson BJ, Willer CJ, Lakka TA, Gybel-Brask DJ, Bustamante M, Hansen T, Pearson ER, Reynolds R, Ostrowski SR, Pennell CE, Jaddoe VWV, Felix JF, Hattersley AT, Melbye M, Lawlor DA, Hveem K, Werge T, Nielsen HS, Magnus P, Evans DM, Jacobsson B, Järvelin MR, Zhang G, Hivert MF, Johansson S†, Freathy RM†, Feenstra B†, Njølstad PR†,$. _ Genome-wide association study of placental weight identifies distinct and shared genetic influences between placental and fetal growth, Nature Genetics, 2023. [PubMed id 37798380] [doi: 10.1038/s41588-023-01520-w] [pdf]

Placental Weight GWAS

The first genome-wide analysis of placental weight. A multi-year meta-analysis from the Early Growth Genetics (EGG) consortium including the Norwegian Mother, Father and Child Cohort Study (MoBa). We provide association results with the genomes of the children and parents, study modes of association, the relationship with birth weight, and to other traits.


  1. Hernández Sánchez LF, Burger B, Castro Campos RA, Johansson S, Njølstad PR, Barsnes H†, Vaudel M†,$. Extending protein interaction networks using proteoforms and small molecules, Bioinformatics, 2023. [PubMed id 37756698] [doi: 10.1093/bioinformatics/btad598] [pdf]

Proteoform network

We study how the structure of pathway-derived interaction networks change upon the inclusion of information on proteoforms and small molecules. We show how accounting for proteoform information allows refining the representation of protein interactions and how small molecules increase the connectivity of the network. But at the same time accounting for this information can create artefacts in the topology of the network.


  1. Burger B$, Vaudel M$, Barsnes H. Importance of Block Randomization When Designing Proteomics Experiments, Journal of Proteome Research, 2020. [PubMed id 32969222] [doi: 10.1021/acs.jproteome.0c00536] [pdf]

Block randomization

A short paper on the principles of block randomization in experimental design. This perspective article aimed at a broad audience is accompanied by a methodological paper on how to design batches for sample processing of cohorts and registries: doi 10.1093/biostatistics/kxac014.


  1. Helgeland Ø1, Vaudel M1, Sole-Navais P, Flatley C, Juodakis J, Bacelis J, Koløen IL, Peggy Knudsen G, Johansson BB, Magnus P, Reichborn Kjennerud T, Juliusson PB, Stoltenberg C, Holmen OL, Andreassen OA, Jacobsson B, Njølstad PR$, Johansson S$. Characterization of the genetic architecture of BMI in infancy and early childhood reveals age-specific effects and implicates pathways involved in Mendelian obesity, Nature Metabolism, 2022. [PubMed id 35315439] [doi: 10.1038/s42255-022-00549-1] [pdf]

Early growth GWAS

Association of BMI during childhood with common variation - we identify different trajectory clusters, time-dependent parent-of-origin effects, and show how the performance of risk scores evolve during early growth.


  1. Hernández Sánchez LF, Burger B, Horro C, Fabregat A, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, Vaudel M$. PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping, GigaScience, 2019. [PubMed id 31363752] [doi: 10.1093/gigascience/giz088] [pdf]

PathwayMatcher

PathwayMatcher can build biological networks of different levels of granularity using the Reactome pathway database, and map different types of omics data to it. Notably, it can build a network to the level of proteoforms, where genes and proteins are separated according to their post-translational state. Hence, interactions are more specific, and interactions between different forms of the same proteins become visible as connections between different nodes, thus providing a new dimension to study biological networks.


Research Articles

  1. Artaza H, Lavrichenko K, Wolff ASB, Røyrvik EC, Vaudel M, Johansson S$. Rare Copy Number Variant analysis in case-control studies using SNP Array Data: a scalable and automated data analysis pipeline, preprint. [Preprint]

  2. Vašíček J, Kuznetsova KG, Skiadopoulou D, Njølstad PR, Johansson S, Bruckner S†, Käll L†, Vaudel M†,$. ProHap enables proteomic database generation accounting for population diversity, preprint. [Preprint]

  3. Lammi V1, Nakanishi T1, Jones SE1, Andrews SJ, Karjalainen J, Cortés B, O’Brien HE, Fulton-Howard BE, Haapaniemi HH, Schmidt A, Mitchell RE, Mousas A, Mangino M, Huerta-Chagoya A, Sinnott-Armstrong N, Cirulli ET, Vaudel M, Kwong ASF, Maiti AK, Marttila M, Batini C, Minnai F, Dearman AR, Warmerdam R, Sequeros CB, Winkler TW, Jordan DM, Guare L, Vergasova E, Marouli E, Striano P, Zainulabid UA, Kumar A, Ahmad HF, Edahiro R, Azekawa S, Long COVID Host Genetics Initiative, FinnGen, DBDS Genomic Consortium, GEN-COVID Multicenter Study, Grzymski JJ, Ishii M, Okada Y, Beckmann ND, Kumari M, Wagner R, Heid IM, John C, Short PJ, Magnus P, Banasik K, Geller F, Franke LH, Rakitko A, Duncan EL, Renieri A, Tsilidis KK, de Cid R, Niavarani A, Tusié-Luna T, Verma SS, Davey Smith G, Timpson NJ, Daly MJ, Ganna A, Schulte EC, Brent Richards J, Ludwig KU, Hultström M, Zeberg H†,$, Ollila HM†,$. Genome-wide Association Study of Long COVID, preprint. [Preprint]

  4. Sole-Navais P1,$, Juodakis J1, Ytterberg K, Xiaoping W, Vaudel M, Helgeland Ø, Flatley C, Geller F, Magnus P, Andreassen OA, Njolstad PR, Feenstra B, Muglia LJ, Johanson S, Jacobsson B$. Genome-wide analysis of neonatal jaundice reveals a marked departure from adult bilirubin metabolism, preprint. [Preprint]

  5. Olwi DI, Kaisinger LR KG, Kentistou KA, Vaudel M, Stankovic S, Njølstad PR, Johansson S, Perry JRB, Day FR, Ong KK†,$. *Likely causal effects of insulin resistance and IGF-1 bioaction on childhood and adult adiposity: a Mendelian randomization study *, International Journal of Obesity, 2024. [PubMed id 39174749] [doi: 10.1038/s41366-024-01605-4] [pdf]

  6. Kentistou KA1, Kaisinger LR1, Stankovic S, Vaudel M, de Oliveira EM, Messina A, Walters RG, Liu X, Busch AS, Helgason H, Thompson DJ, Santon F, Petricek KM, Zouaghi Y, Huang-Doran I, Gudbjartsson DF, Bratland E, Lin K, Gardner EJ, Zhao Y, Jia R, Terao C, Riggan M, Bolla MK, Yazdanpanah M, Yazdanpanah N, Bradfield JP, Broer L, Campbell A, Chasman DI, Cousminer DL, Franceschini N, Franke LH, Girotto G, He C, Järvelin MR, Joshi PK, Kamatani Y, Karlsson R, Luan J, Lunetta KL, Mägi R, Mangino M, Medland SE, Meisinger C, Noordam R, Nutile T, Concas MP, Polašek O, Porcu E, Ring SM, Sala C, Smith AV, Tanaka T, van der Most PJ, Vitart V, Wang CA, Willemsen G, Zygmunt M, Ahearn TU, Andrulis IL, Anton-Culver H, Antoniou AC, Auer PL, Barnes CL, Beckmann MW, Berrington A, Bogdanova NV, Bojesen SE, Brenner H, Buring JE, Canzian F, Chang-Claude J, Couch FJ, Cox A, Crisponi L, Czene K, Daly MB, Demerath EW, Dennis J, Devilee P, Vivo I, Dörk T, Dunning AM, Dwek M, Eriksson JG, Fasching PA, Fernandez-Rhodes L, Ferreli L, Fletcher O, Gago-Dominguez M, García-Closas M, García-Sáenz JA, González-Neira A, Grallert H, Guénel P, Haiman CA, Hall P, Hamann U, Hakonarson H, Hart RJ, Hickey M, Hooning MJ, Hoppe R, Hopper JL, Hottenga JJ, Hu FB, Hubner H, Hunter DJ, ABCTB Investigators, Jernstrom H, John EM, Karasik D, Khusnutdinova EK, Kristensen VN, Lacey JV, Lambrechts D, Launer LJ, Lind PA, Lindblom A, Magnusson PKE, Mannermaa A, McCarthy mi, Meitinger T, Menni C, Michailidou K, Millwood IY, Milne RL, Montgomery GW, Nevanlinna H, Nolte IM, Nyholt DR, Obi N, O’Brien KM, Offit K, Oldehinkel AJ, Ostrowski SR, Palotie A, Pedersen OB, Peters A, Pianigiani G, Plaseska-Karanfilska D, Pouta A, Pozarickij A, Radice P, Rennert G, Rosendaal FR, Ruggiero D, Saloustros E, Sandler DP, Schipf S, Schmidt CO, Schmidt MK, Small K, Spedicati B, Stampfer M, J Stone, Tamimi RM, TerasLR, Tikkanen E, Turman C, Vachon CM, Wang Q, Winqvist R, Wolk A, Zemel BS, Zheng W, van Dijk KW, Alizadeh BZ, Bandinelli S, Boerwinkle E, Boomsma DI, Ciullo M, Chenevix-Trench G, Cucca F, Esko T, Gieger C, Grant SFA, Gudnason V, Hayward C, Kolcic I, Kraft P, Lawlor DA, Martin NG, Nohr EA, Pedersen NL, Pennell CE, Ridker PM, Robino A, Snieder H, Sovio U, Spector TD, Stockl D, Sudlow C, Timpson NJ, Toniolo D, Uitterlinden A, Ulivi S, VolzkeH, Wareham NJ, Widen E, Wilson JF, The Lifelines Cohort Study, The Danish Blood Donor study, The Ovarian Cancer Association Consortium, The Breast Cancer Association Consortium, The Biobank Japan Project, The China Kadoorie Biobank Collaborative Group, Pharoah PDP, Li L, Easton DF, Njølstad pr, Sulem P, Murabito JM, Murray A, Manousaki D, Juul A, ErikstrupC, Stefansson K, Horikoshi M, Chen Z, Farooqi IS, Pitteloud N, JohanssonS, Day FR†, Perry JRB†,$, Ong KK†. Understanding the genetic complexity of puberty timing across the allele frequency spectrum, Nature Genetics, 2024. [PubMed id 38951643] [doi: 10.1038/s41588-024-01798-4] [pdf]

  7. Kuznetsova KG$, Vašíček J, Skiadopoulou D, Molnes J, Udler M, Johansson S, Njølstad PR, Manning A†, Vaudel M†,$. A systematic mapping of the genomic and proteomic variation associated with monogenic diabetes, Plos One, 2024. [PubMed id 38635808] [doi: 10.1371/journal.pone.0300350] [pdf]

  8. Jaitner A, Vaudel M, Tsaneva-Atanasova K, Njølstad PR, Jacobsson B, Bowden J, Johansson S, Freathy R$. Smoking during pregnancy and its effect on placental weight: A Mendelian randomization study, BMC Pregnancy Childbirth, 2024. [PubMed id 38575863] [doi: 10.1186/s12884-024-06431-0] [pdf]

  9. Artaza H, Eriksson D, Lavrichenko K, Aranda-Guillén M, Bratland E, Vaudel M, Knappskog P, Husebye E, Bensing S, Wolff ASB, Kämpe O, Røyrvik EC$, Johansson S$. Rare copy number variation in autoimmune Addison’s disease, Frontiers in Immunology, 2024. [PubMed id 38562931] [doi: 10.3389/fimmu.2024.1374499] [pdf]

  10. Vašíček J1, Skiadopoulou D1, Kuznetsova KG, Wen B, Johansson S, Njølstad PR, Bruckner S, Käll L†, Vaudel M†,$. Finding Haplotypic Signatures in Proteins, GigaScience, 2023. [PubMed id 37919975] [doi: 10.1093/gigascience/giad093] [pdf]

  11. Beaumont RN1, Flatley C1, Vaudel M1, Xiaoping W, Chen J, Moen GH, Skotte L, Helgeland Ø, Sole-Navais P, Banasik K, Albiñana C, Ronkainen J, Fadista J, Stinson SE, Trajanoska K, Wang CA, Westergaard D, Srinivasan S, Sánchez-Soriano C, Bilbao JR, Allard C, Groleau M, Kuulasmaa T, Leirer DJ, White F, Jacques PE, Cheng H, Hao K, Andreassen OA, Åsvold BO, Atalay M, Bhatta L, Bouchard L, Brumpton BM, Brunak S, Bybjerg-Grauholm J, Ebbing C, Elliott P, Engelbrechtsen L, Erikstrup C, Estarlich M, Franks S, Gaillard R, Geller F, Grove J, Hougaard DM, Kajantie E, Morgen CS, Nohr EA, Nyegaard M, Palmer CNA, Pedersen OB, The Early Growth Genetics (EGG) Consortium, Rivadeneira F, Sebert S, Shields BM, Stoltenberg C, Surakka I, Thørner LW, Ullum H, Vaarasmaki M, Vilhjalmsson BJ, Willer CJ, Lakka TA, Gybel-Brask DJ, Bustamante M, Hansen T, Pearson ER, Reynolds R, Ostrowski SR, Pennell CE, Jaddoe VWV, Felix JF, Hattersley AT, Melbye M, Lawlor DA, Hveem K, Werge T, Nielsen HS, Magnus P, Evans DM, Jacobsson B, Järvelin MR, Zhang G, Hivert MF, Johansson S†, Freathy RM†, Feenstra B†, Njølstad PR†,$. Genome-wide association study of placental weight identifies distinct and shared genetic influences between placental and fetal growth, Nature Genetics, 2023. [PubMed id 37798380] [doi: 10.1038/s41588-023-01520-w] [pdf]

  12. Hernández Sánchez LF, Burger B, Castro Campos RA, Johansson S, Njølstad PR, Barsnes H†, Vaudel M†,$. Extending protein interaction networks using proteoforms and small molecules, Bioinformatics, 2023. [PubMed id 37756698] [doi: 10.1093/bioinformatics/btad598] [pdf]

  13. Skiadopoulou D, Vašíček J, Kuznetsova KG, Käll L†, Vaudel M†,$. Retention time and fragmentation predictors increase confidence in variant peptide identification, Journal of Proteome Research, 2023. [PubMed id 37656829] [doi: 10.1021/acs.jproteome.3c00243] [pdf]

  14. Sole-Navais P$, Flatley C, Steinthorsdottir V, Vaudel M, Chen J, Laisk T, LaBella AL, Westergaard D, Bacelis J, Juodakis J, Brumpton B, Skotte L, Borges MC, Helgeland Ø, Mahajan A, Wielscher M, Lin F, Briggs C, Wang CA, Moen GH, Beaumont RN, Bradfield JP, Thorleifsson G, Elvestad Gabrielsen M, Rye Ostrowski S, Modzelewska D, Estonian Biobank Research Team, Nohr EA, Hypponen E, Srivastava A, Talbot O, Allard C, Williams SM, Menon R, Shields BM, Sveinbjornsson G, Xu H, Danish Blood Donor Study Genomic Consortium, Early Growth Genetics Consortium, Melbye M, William L Jr, Bouchard L, Oken E, Birger Pedersen O, Gudbjartsson DF, Erikstrup C, Sorensen E, Lie RT, Teramo K, Hallman M, Juliusdottir T, Hakonarson H, Hattersley AT, Sletner L, Merialdi M, Rifas-Shiman S, Steingrimsdottir T, Scholtens D, Power C, West J, Nyegaard M, Capra JA, Skogholt AH, Magnus P, Andreassen OA, Thorsteinsdottir U, Grant SFA, Qvigstad E, Pennell CE, Hivert MF, Hayes GM, Jarvelin MR, McCarthy MI, Lawlor DA, Lawlor DA, Nielsen HS, Magi R, Rokas A, Hveem K, Stefansson K, Feenstra B, Njolstad PR, Muglia LJ, Freathy RM, Johanson S, Zhang G†, Jacobsson B†,$. Genetic effects on the timing of parturition and links to fetal birth weight, Nature Genetics, 2023. [PubMed id 37012456] [doi: 10.1038/s41588-023-01343-9] [pdf]

  15. Burger B$, Vaudel M, Barsnes H. Automated splitting into batches for observational biomedical studies with sequential processing, Biostatistics, 2022. [PubMed id 35536588] [doi: 10.1093/biostatistics/kxac014] [pdf]

  16. Helgeland Ø1, Vaudel M1, Sole-Navais P, Flatley C, Juodakis J, Bacelis J, Koløen IL, Knudsen GP, Johansson BB, Magnus P, Kjennerud TR, Juliusson PB, Stoltenberg C, Holmen OL, Andreassen OA, Jacobsson B, Njølstad PR$, Johansson S$. Characterization of the genetic architecture of infant and early childhood body mass index, Nature Metabolism, 2022. [PubMed id 35315439] [doi: 10.1038/s42255-022-00549-1] [pdf]

  17. Carrasco M, Wang C, Søviknes AM, Bjørlykke Y, Abadpour S, Paulo JA, Tjora E, Njølstad P, Ghabayen J, Nermoen I, Lyssenko V, Chera S, Ghila LM, Vaudel M, Scholz H, Ræder H$. Spatial Environment Affects HNF4A Mutation-Specific Proteome Signatures and Cellular Morphology in hiPSC-Derived β-Like Cells, Diabetes, 2022. [PubMed id 35043148] [doi: 10.2337/db20-1279] [pdf]

  18. Flatley C$, Sole-Navais P, Vaudel M, Helgeland Ø, Modzelewska D, Johansson S, Jacobsson B†, Njølstad P†. Placental weight centiles adjusted for age, parity and fetal sex, Placenta, 2022. [PubMed id 34773745] [doi: 10.1016/j.placenta.2021.10.011] [pdf]

  19. Farag YM, Horro C, Vaudel M, Barsnes H$. PeptideShaker Online: A User-Friendly Web-Based Framework for the Identification of Mass Spectrometry-Based Proteomics Data, Journal of Proteome Research, 2021. [PubMed id 34709836] [doi: 10.1021/acs.jproteome.1c00678] [pdf]

  20. Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M$, Sachsenberg T$, Levitsky LI$, Perez-Riverol Y$. A proteomics sample metadata representation for multiomics integration and big data analysis, Nature Communications, 2021. [PubMed id 34615866] [doi: 10.1038/s41467-021-26111-3] [pdf]

  21. Eriksson D1, Røyrvik EC1, Aranda-Guillén M1, Berger AH, Landegren N, Artaza H, Hallgren Å, Grytaas MA, Ström S, Bratland E, Botusan IR, Oftedal BE, Breivik L, Vaudel M, Helgeland Ø, Falorni A, Jørgensen AP, Hulting A-L, Svartberg J, Ekwall O, Fougner KJ, Wahlberg J, Nedrebø BG, Dahlqvist P, The Norwegian Addison Registry Study Group, The Swedish Addison Registry Study Group, Knappskog PM, Bøe AS, Bensing S, Johansson S†, Kämpe O†,$, Husebye ES†,$. GWAS for autoimmune Addison’s disease identifies multiple risk loci and highlights AIRE in disease susceptibility, Nature Communications, 2021. [PubMed id 33574239] [doi: 10.1038/s41467-021-21015-8] [pdf]

  22. Sole-Navais P$, Bacelis J, Helgeland Ø, Modzelewska D, Vaudel M, Flatley C, Andreassen O, Njølstad PR, Muglia LJ, Johansson S, Zhang G, Jacobsson B. Autozygosity mapping and time-to-spontaneous delivery in Norwegian parent-offspring trios, Human Molecular Genetics, 2020. [PubMed id 33291140] [doi: 10.1093/hmg/ddaa255] [pdf]

  23. Gupta MK, Vethe H, Softic S, Rao TN, Wagh V, Shirakawa J, Barsnes H, Vaudel M, Takatani T, Kahraman S, Sakaguchi M, Martinez R, Hu J, Bjørlykke Y, Raeder H, Kulkarni RN$. Leptin Receptor Signaling Regulates Protein Synthesis Pathways and Neuronal Differentiation in Pluripotent Stem Cells, Stem Cell Reports, 2020. [PubMed id 33125875] [doi: 10.1016/j.stemcr.2020.10.001] [pdf]

  24. Vogelezang S1, Bradfield JP1, Ahluwalia TS, Curtin JA, Lakka TA, Grarup N, Scholz M, van der Most PJ, Monnereau C, Stergiakouli E, Heiskala A, Horikoshi M, Fedko IO, Vilor-Tejedor N, Cousminer DL, Standl M, Wang CA, Viikari J, Geller F, Íñiguez C, Pitkänen N, Chesi A, Bacelis J, Yengo L, Torrent M, Ntalla I, Helgeland Ø, Selzam S, Vonk JM, Zafarmand MH, Heude B, Farooqi IS, Alyass A, Beaumont RN, Have CT, Rzehak P, Bilbao JR, Schnurr TM, Barroso I, Bønnelykke K, Beilin LJ, Carstensen L, Charles MA, Chawes B, Clément K, Closa-Monasterolo R, Custovic A, Eriksson JG, Escribano J, Groen-Blokhuis M, Grote V, Gruszfeld D, Hakonarson H, Hansen T, Hattersley AT, Hollensted M, Hottenga JJ, Hyppönen E, Johansson S, Joro R, Kähönen M, Karhunen V, Kiess W, Knight BA, Koletzko B, Kühnapfel A, Landgraf K, Langhendries JP, Lehtimäki T, Leinonen JT, Li A, Lindi V, Lowry E, Bustamante M, Medina-Gomez C, Melbye M, Michaelsen KF, Morgen CS, Mori TA, Nielsen TRH, Niinikoski H, Oldehinkel AJ, Pahkala K, Panoutsopoulou K, Pedersen O, Pennell CE, Power C, Reijneveld SA, Rivadeneira F, Simpson A, Sly PD, Stokholm J, Teo KK, Thiering E, Timpson NJ, Uitterlinden AG, van Beijsterveldt CEM, van Schaik BDC, Vaudel M, Verduci E, Vinding RK, Vogel M, Zeggini E, Sebert S, Lind MV, Brown CD, Santa-Marina L, Reischl E, Frithioff-Bøjsøe C, Meyre D, Wheeler E, Ong K, Nohr EA, Vrijkotte TGM, Koppelman GH, Plomin R, Njølstad PR, Dedoussis GD, Froguel P, Sørensen TIA, Jacobsson B, Freathy RM, Zemel BS, Raitakari O, Vrijheid M, Feenstra B, Lyytikäinen LP, Snieder H, Kirsten H, Holt PG, Heinrich J, Widén E, Sunyer J, Boomsma DI, Järvelin MR, Körner A, Davey Smith G, Holm JC, Atalay M, Murray C, Bisgaard H, McCarthy MI; Early Growth Genetics Consortium, Jaddoe VWV†, Grant SFA†, Felix JF†,$. Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits, PLoS Genetics, 2020. [PubMed id 33045005] [doi: 10.1371/journal.pgen.1008718] [pdf]

  25. Smajlagić D, Lavrichenko K, Berland S, Helgeland Ø, Knudsen GP, Vaudel M, Haavik J, Knappskog PM, Njølstad PR, Houge G, Johansson S$. Population prevalence and inheritance pattern of recurrent CNVs associated with neurodevelopmental disorders in 12,252 newborns and their parents, European Journal of Human Genetics, 2020. [PubMed id 32778765] [doi: 10.1038/s41431-020-00707-7] [pdf]

  26. Aasebø E, Berven FS, Bartaula-Brevik S, Stokowy T, Hovland R, Vaudel M, Døskeland SO, McCormack E, Batth TS, Olsen JV, Bruserud Ø, Selheim F†, Hernandez-Valladares M†,$. Proteome and Phosphoproteome Changes Associated with Prognosis in Acute Myeloid Leukemia, Cancers, 2020. [PubMed id 32192169] [doi: 10.3390/cancers12030709] [pdf]

  27. Loo LSW, Vethe H, Soetedjo AAP, Paulo JA, Jasmen J, Jackson N, Bjørlykke Y, Valdez IA, Vaudel M, Barsnes H, Gygi SP, Ræder H, Teo AKK$, Kulkarni RN$. Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors, Stem Cells, 2019. [PubMed id 31828876] [doi: 10.1002/stem.3135] [pdf]

  28. Bjørlykke Y, Søviknes AM, Hoareau L, Vethe H, Mathisen AF, Chera S, Vaudel M, Ghila L, Ræder H$. Reprogrammed cells display distinct proteomic signatures associated with colony morphology variability, Stem Cells International, 2019. [PubMed id 31827534] [doi: 10.1155/2019/8036035] [pdf]

  29. Qiao Z, Zheng J, Helgeland Ø, Vaudel M, Johansson S, Njølstad PR, Davey Smith G, Warrington NM, Evans D$. Introducing M-GCTA a software package to estimate maternal (or paternal) genetic effects on offspring phenotypes, Behavior Genetics, 2019. [PubMed id 31493278] [doi: 10.1007/s10519-019-09969-4] [pdf (accepted version)] [Request a reprint]

  30. Hernández Sánchez LF, Burger B, Horro C, Fabregat A, Johansson S, Njølstad PR, Barsnes H, Hermjakob H, Vaudel M$. PathwayMatcher: proteoform-centric network construction enables fine-granularity multi-omics pathway mapping, GigaScience, 2019. [PubMed id 31363752] [doi: 10.1093/gigascience/giz088] [pdf]

  31. Helgeland Ø, Vaudel M, Juliusson PB, Lingaas Holmen O, Juodakis J, Bacelis J, Jacobsson B, Lindekleiv H, Hveem K, Lie RT, Knudsen GP, Stoltenberg C, Magnus P, Sagen JV, Molven A, Johansson S†$, Njølstad PR†$. Genome-wide association study reveals a dynamic role of common genetic variation in infant and early childhood growth, Nature Communications, 2019. [PubMed id 31575865] [Preprint] [doi: 10.1038/s41467-019-12308-0] [pdf]

  32. Bradfield JP1, Vogelezang S1, Felix JF, Chesi A, Helgeland Ø, Horikoshi M, Karhunen V, Lowry E, Cousminer DL, Ahluwalia TS, Thiering E, Boh ET, Zafarmand MH, Vilor-Tejedor N, Wang CA, Joro R, Chen Z, Gauderman WJ, Pitkänen N, Parra EJ, Fernandez-Rhodes L, Alyass A, Monnereau C, Curtin JA, Have CT, McCormack SE, Hollensted M, Frithioff-Bøjsøe C, Valladares-Salgado A, Peralta-Romero J, Teo YY, Standl M, Leinonen JT, Holm JC, Peters T, Vioque J, Vrijheid M, Simpson A, Custovic A, Vaudel M, Canouil M, Lindi V, Atalay M, Kähönen M, Raitakari OT, van Schaik BDC, Berkowitz RI, Cole SA, Voruganti VS, Wang Y, Highland HM, Comuzzie AG, Butte NF, Justice AE, Gahagan S, Blanco E, Lehtimäki T, Lakka TA, Hebebrand J, Bonnefond A, Grarup N, Froguel P, Lyytikäinen LP, Cruz M, Kobes S, Hanson RL, Zemel BS, Hinney A, Teo KK, Meyre D, North KE, Gilliland FD, Bisgaard H, Bustamante M, Bonnelykke K, Pennell CE, Rivadeneira F, Uitterlinden AG, Baier LJ, Vrijkotte TGM, Heinrich J, Sørensen TIA, Saw SM, Pedersen O, Hansen T, Eriksson J, Widén E, McCarthy MI, Njølstad PR, Power C, Hyppönen E, Sebert S, Brown CD, Järvelin MR, Timpson NJ, Johansson S, Hakonarson H, Jaddoe VWV†; Early Growth Genetics Consortium, Grant SFA†,$. A Trans-ancestral Meta-Analysis of Genome-Wide Association Studies Reveals Loci Associated with Childhood Obesity, Human Molecular Genetics, 2019. [PubMed id 31504550] [doi: 10.1093/hmg/ddz161] [pdf]

  33. Warrington NM1, Beaumont RN1, Horikoshi M1, Day FR1, Helgeland Ø1, Laurin C, Bacelis J, Peng S, Hao K, Feenstra B, Wood AR, Mahajan A, Tyrrell J, Robertson NR, Rayner NW, Qiao Z, Moen GH, Vaudel M, Marsit CJ, Chen J, Nodzenski M, Schnurr TM, Zafarmand MH, Bradfield JP, Grarup N, Kooijman MN, Li-Gao R, Geller F, Ahluwalia TS, Paternoster L, Rueedi R, Huikari V, Hottenga JJ, Lyytikäinen LP, Cavadino A, Metrustry S, Cousminer DL, Wu Y, Thiering E, Wang CA, Have CT, Vilor-Tejedor N, Joshi PK, Painter JN, Ntalla I, Myhre R, Pitkänen N, van Leeuwen EM, Joro R, Lagou V, Richmond RC, Espinosa A, Barton SJ, Inskip HM, Holloway JW, Santa-Marina L, Estivill X, Ang W, Marsh JA, Reichetzeder C, Marullo L, Hocher B, Lunetta KL, Murabito JM, Relton CL, Kogevinas M, Chatzi L, Allard C, Bouchard L, Hivert MF, Zhang G, Muglia LJ, Heikkinen J; EGG Consortium, Morgen CS, van Kampen AHC, van Schaik BDC, Mentch FD, Langenberg C, Luan J, Scott RA, Zhao JH, Hemani G, Ring SM, Bennett AJ, Gaulton KJ, Fernandez-Tajes J, van Zuydam NR, Medina-Gomez C, de Haan HG, Rosendaal FR, Kutalik Z, Marques-Vidal P, Das S, Willemsen G, Mbarek H, Müller-Nurasyid M, Standl M, Appel EVR, Fonvig CE, Trier C, van Beijsterveldt CEM, Murcia M, Bustamante M, Bonas-Guarch S, Hougaard DM, Mercader JM, Linneberg A, Schraut KE, Lind PA, Medland SE, Shields BM, Knight BA, Chai JF, Panoutsopoulou K, Bartels M, Sánchez F, Stokholm J, Torrents D, Vinding RK, Willems SM, Atalay M, Chawes BL, Kovacs P, Prokopenko I, Tuke MA, Yaghootkar H, Ruth KS, Jones SE, Loh PR, Murray A, Weedon MN, Tönjes A, Stumvoll M, Michaelsen KF, Eloranta AM, Lakka TA, van Duijn CM, Kiess W, Körner A, Niinikoski H, Pahkala K, Raitakari OT, Jacobsson B, Zeggini E, Dedoussis GV, Teo YY, Saw SM, Montgomery GW, Campbell H, Wilson JF, Vrijkotte TGM, Vrijheid M, de Geus EJCN, Hayes MG, Kadarmideen HN, Holm JC, Beilin LJ, Pennell CE, Heinrich J, Adair LS, Borja JB, Mohlke KL, Eriksson JG, Widén EE, Hattersley AT, Spector TD, Kähönen M, Viikari JS, Lehtimäki T, Boomsma DI, Sebert S, Vollenweider P, Sørensen TIA, Bisgaard H, Bønnelykke K, Murray JC, Melbye M, Nohr EA, Mook-Kanamori DO, Rivadeneira F, Hofman A, Felix JF, Jaddoe VWV, Hansen T, Pisinger C, Vaag AA, Pedersen O, Uitterlinden AG, Järvelin MR, Power C, Hyppönen E, Scholtens DM, Lowe WL Jr, Davey Smith G, Timpson NJ, Morris AP, Wareham NJ, Hakonarson H, Grant SFA, Frayling TM, Lawlor DA, Njølstad PR, Johansson S, Ong KK†, McCarthy MI†, Perry JRB†, Evans DM†,$, Freathy RM†,$. Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors, Nature Genetics, 2019. [PubMed id 31043758] [Preprint] [doi: 10.1038/s41588-019-0403-1] [pdf]

  34. Zhang-James Y, Vaudel M, Mjaavatten O, Berven FS, Haavik J, Faraone SV. Effect of disease-associated SLC9A9 mutations on protein-protein interaction networks: implications for molecular mechanisms for ADHD and autism, ADHD Attention Deficit and Hyperactivity Disorders, 2019. [PubMed id 30927234] [doi: 10.1007/s12402-018-0281-x] [No Open Access found Request a reprint]

  35. Burger B, Hernández Sánchez LF, Lereim RR, Barsnes H, Vaudel M$. Analyzing the Structure of Pathways and Its Influence on the Interpretation of Biomedical Proteomics Data Sets, Journal of Proteome Research, 2018. [PubMed id 30251541] [Preprint] [doi: 10.1021/acs.jproteome.8b00464] [pdf]

  36. Barsnes H, Vaudel M$. SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines, Journal of Proteome Research, 2018. [PubMed id 29774740] [doi: 10.1021/acs.jproteome.8b00175] [pdf]

  37. Li K, Vaudel M, Zhang B, Ren Y, Wen B$. PDV: an integrative proteomics data viewer, Bioinformatics, 2018. [PubMed id 30169737] [doi: 10.1093/bioinformatics/bty770] [pdf]

  38. Kopczynski D, Barsnes H, Njølstad PR, Sickmann A, Vaudel M$, Ahrends R$. PeptideMapper: Efficient and Versatile Amino Acid Sequence and Tag Mapping, Bioinformatics, 2017. [PubMed id 28334306] [doi: 10.1093/bioinformatics/btx122] [pdf]

  39. Berland S, Toft Bertelsen TL, Aukrust I, Byška J, Vaudel M, MacAulay N, Houge G$. A de novo Ser111Thr in aquaporin-4 in a patient with transient brain edema, transient heart failure, intellectual disability and slowly progressive brain dysfunction, Molecular Case Studies, 2017. [PubMed id 29437797] [doi: 10.1101/mcs.a002303] [pdf]

  40. Beaumont RN1, Warrington NM1, Cavadino A, Tyrrell J, Nodzenski M, Horikoshi M, Geller F, Myhre R, Richmond RC, Paternoster L, Bradfield JP, Kreiner-Møller E, Huikari V, Metrustry S, Lunetta KL, Painter JN, Hottenga JJ, Allard C, Barton SJ, Espinosa A, Marsh JA, Potter C, Zhang G, Ang W, Berry DJ, Bouchard L, Das S; Early Growth Genetics (EGG) Consortium, Hakonarson H, Heikkinen J, Helgeland Ø, Hocher B, Hofman A, Inskip HM, Jones SE, Kogevinas M, Lind PA, Marullo L, Medland SE, Murray A, Murray JC, Njølstad PR, Nohr EA, Reichetzeder C, Ring SM, Ruth KS, Santa-Marina L, Scholtens DM, Sebert S, Sengpiel V, Tuke MA, Vaudel M, Weedon MN, Willemsen G, Wood AR, Yaghootkar H, Muglia LJ, Bartels M, Relton CL, Pennell CE, Chatzi L, Estivill X, Holloway JW, Boomsma DI, Montgomery GW, Murabito JM, Spector TD, Power C, Järvelin MR, Bisgaard H, Grant SFA, Sørensen TIA, Jaddoe VW, Jacobsson B, Melbye M, McCarthy MI, Hattersley AT, Hayes MG, Frayling TM, Hivert MF, Felix JF, Hyppönen E, Lowe WL Jr, Evans DM†, Lawlor DA†,$, Feenstra B†,$, Freathy RM†,$.. Genome-wide association study of offspring birth weight in 86,577 women highlights maternal genetic effects that are independent of fetal genetics, Human Molecular Genetics, 2017. [PubMed id 29309628] [doi: 10.1101/mcs.a002303] [pdf]

  41. Chambers MC, Jagtap PD, Johnson JE, McGowan T, Kumar P, Onsongo G, Guerrero CR, Barnses H, Vaudel M, Martens L, Grüning BA, Cooke IR, Heydarian M, Reddy KL, Griffin TJ$. An accessible proteogenomics informatics resource for cancer researchers, Cancer Research, 2017. [PubMed id 29092937] [doi: 10.1158/0008-5472.CAN-17-0331] [pdf]

  42. Vizcaíno JA, Meyer G, Perkins SR, Barsnes H, Vaudel M, Perez-Riverol Y, Terment T, Uszkoreit J, Eineacher M, Fischer L, Rappsilber J, Netz E, Walzer M, Kohlbacher O, Leitner A, Chalkley RJ, Ghali F, Martínez-Bartolomé S, Deutsch EW, Johnes AR$. The mzIdentML data standard version 1.2, supporting advances in proteome informatics, Mol Cell Proteomics, 2017. [PubMed id 28515314] [doi: 10.1074/mcp.M117.068429] [pdf]

  43. Leprevost FdV, Aflitos SA, Grüning BA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeufferz J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y$. BioContainers: An open-source and community-driven framework for software standardization, Bioinformatics, 2017. [PubMed id 28379341] [doi: 10.1093/bioinformatics/btx192] [pdf]

  44. Kroksveen AC$, Guldbrandsen A, Vaudel M, Lereim RR, Barsnes H, Myr KM, Torkildsen Ø, Berven FS$. In-Depth Cerebrospinal Fluid Quantitative Proteome and Deglycoproteome Analysis: Presenting a Comprehensive Picture of Pathways and Processes Affected by Multiple Sclerosis, Journal of Proteome Research, 2017. [PubMed id 27728768] [doi: 10.1021/acs.jproteome.6b00659] [No Open Access found Request a reprint]

  45. Hernandez-Valladares M1,$, Aasebø E1, Mjaavatten O, Vaudel M, Bruserud Ø, Berven FS, Selheim F. Reliable FASP-based procedures for optimal quantitative proteomic and phosphoproteomic analysis on samples from acute myeloid leukemia patients, Biol Proced Online, 2016. [PubMed id 27330413] [doi: 10.1186/s12575-016-0043-0] [pdf]

  46. Aasebø E1, Mjaavatten O, Vaudel M, Farag Y, Selheim F, Berven FS, Bruserud Ø, Hernandez-Valladares M1,$. Freezing effects on the acute myeloid leukemia cell proteome and phosphoproteome revealed using optimal quantitative workflows, Journal of Proteomics, 2016. [PubMed id 27107777] [doi: 10.1016/j.jprot.2016.03.049] [No Open Access found Request a reprint]

  47. Opsahl JA, Vaudel M, Guldbrandsen A, Aasebø E, Van Pesch V, Franciotta D, Myhr KM, Barsnes H, Berle M, Torkildsen Ø, Kroksveen AC, Berven FS$. Label free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis, Proteomics, 2016. [PubMed id 26841090] [doi: 10.1002/pmic.201500284] [No Open Access found Request a reprint]

  48. Vaudel M, Burkhart JM, Zahedi RP, Oveland E, Berven FS, Sickmann A, Martens L$, Barsnes H. PeptideShaker enables reanalysis of mass spectrometry-derived proteomics datasets, Nature Biotechnology, 2015. [PubMed id 25574629] [doi: 10.1038/nbt.3109] [pdf (accepted version)] [Request a reprint]

  49. Verheggen K, Maddelein D, Hulstaert N, Martens L$, Barsnes H, Vaudel M. Pladipus enables universal distributed computing in proteomics bioinformatics, Journal of Proteome Research, 2015. [PubMed id 26510693] [doi: 10.1021/acs.jproteome.5b00850] [pdf]

  50. Barsnes H$, Vaudel M, Martens L. JSparklines: Making tabular proteomics data come alive, Proteomics, 2015. [PubMed id 25422159] [doi: 10.1002/pmic.201400356] [No Open Access found Request a reprint]

  51. Bjørlykke Y, Vethe H, Vaudel M, Barsnes H, Berven FS, Tjora E, Raeder H$. Carboxyl-Ester Lipase Maturity-Onset Diabetes of the Young Disease Protein Biomarkers in Secretin-Stimulated Duodenal Juice, Journal of Proteome Research, 2015. [PubMed id 25369532] [doi: 10.1021/pr500750z] [No Open Access found Request a reprint]

  52. Muth T1, Weilnböck L1, Rapp E, Huber CG, Martens L, Vaudel M$, Barsnes H. DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra, Journal of Proteome Research, 2014. [PubMed id 24295440] [doi: 10.1021/pr4008078] [pdf]

  53. Helgeland E, Breivik LE, Vaudel M, Svendsen OS, Garberg H, Nordrehaug JE, Berven FS, Jonassen AK$. Exploring the human plasma proteome for humoral mediators of remote ischemic preconditioning - a word of caution, PLoS One, 2014. [PubMed id 25333471] [doi: 10.1371/journal.pone.0109279] [pdf]

  54. Vethe H, Finne K, Skogstrand T, Vaudel M, Vikse BE, Hultström M, Placier S, Scherer A, Tenstad O, Marti HP$. Distinct protein signature of hypertension-induced damage in the renal proteome of the two-kidney, one-clip rat model, Journal of Hypertension, 2015. [PubMed id 25304470] [doi: 10.1097/HJH.0000000000000370] [No Open Access found Request a reprint]

  55. Aasebø E, Vaudel M, Mjaavatten O, Gaudsdal G, Van der Burgh A, Gjertsen BT, Døskeland SO, Brusserud O, Berven FS, Selheim F$. Performance of super-SILAC based quantitative proteomics for comparison of different acute myeloid leukemia (AML) cell lines, Proteomics, 2014. [PubMed id 25044641] [doi: 10.1002/pmic.201300448] [No Open Access found Request a reprint]

  56. Vaudel M, Venne S, Berven FS, Zahedi RP, Martens L, Barsnes H$. Shedding light on black boxes in protein identification, Proteomics, 2014. [PubMed id 24678044] [doi: 10.1002/pmic.201300488] [pdf]

  57. Beck F, Geiger J, Gambaryan S, Veit J, Vaudel M, Nollau P, Kohlbacher O, Martens L, Walter U, Sickmann A$, Zahedi RP$. Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways, Blood, 2014. [PubMed id 24324209] [doi: 10.1182/blood-2013-07-512384] [pdf]

  58. Vaudel M, Breiter D, Beck F, Rahnenführer J, Martens L$, Zahedi RP. D-score: a search engine independent MD-score, Proteomics, 2013. [PubMed id 23307401] [doi: 10.1002/pmic.201200408] [pdf (accepted version)] [Request a reprint]

  59. Burkhart JM1, Vaudel M1, Gambaryan S, Radau S, Walter U, Martens L, Geiger J$, Sickmann A, and Zahedi RP$. The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways in human platelets, Blood, 2012. [PubMed id 22869793] [doi: 10.1182/blood-2012-04-416594] [pdf]

  60. Vaudel M1, Burkhart JM1, Radau S, Zahedi RP, Martens L$, Sickmann A. Integral Quantification Accuracy estimation for Reporter Ion based quantitative proteomics (iQuARI), Journal of Proteome Research, 2012. [PubMed id 22874012] [doi: 10.1021/pr300247u] [No Open Access found Request a reprint]

  61. Vaudel M1, Burkhart JM1, Breiter D, Zahedi RP, Sickmann A$, Martens L. A complex standard for protein identification, designed by evolution, Journal of Proteome Research, 2012. [PubMed id 22489649] [doi: 10.1021/pr300055q] [No Open Access found Request a reprint]

  62. Vaudel M1, Barsnes H1,$, Berven FS, Sickmann A, Martens L. SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches, Proteomics, 2011. [PubMed id 21337703] [doi: 10.1002/pmic.201000595] [pdf (accepted version)] [Request a reprint]

  63. Colaert N, Barsnes H, Vaudel M, Helsens K, Timmerman E, Sickmann A, Gevaert K, Martens L$. Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files, Journal of Proteome Research, 2011. [PubMed id 21714566] [doi: 10.1021/pr2005154] [pdf]

  64. Vaudel M1, Burkhart JM1, Sickmann A, Martens L$, Zahedi RP. Peptide identification quality control, Proteomics, 2011. [PubMed id 21500347] [doi: 10.1002/pmic.201000704] [No Open Access found Request a reprint]

  65. Barsnes H, Vaudel M, Colaert N, Helsens K, Sickmann A, Berven FS, Martens L$. compomics-utilities: an open-source Java library for computational proteomics, BMC Bioinformatics, 2011. [PubMed id 21385435] [doi: 10.1186/1471-2105-12-70] [pdf]

  66. Burkhart JM1, Vaudel M1, Zahedi RP, Martens L, Sickmann A$. iTRAQ protein quantification: a quality-controlled workflow, Proteomics, 2011. [PubMed id 21328540] [doi: 10.1002/pmic.201000711] [No Open Access found Request a reprint]

  67. Muth T, Vaudel M, Barsnes H, Martens L$, Sickmann A. XTandem Parser: An open-source library to parse and analyse X!Tandem MS/MS search results, Proteomics, 2010. [PubMed id 20140905] [doi: 10.1002/pmic.200900759] [No Open Access found Request a reprint]


Outreach - Proceeding

  1. Burger B$, Vaudel M$, Barsnes H. Importance of Block Randomization When Designing Proteomics Experiments, Journal of Proteome Research, 2020. [PubMed id 32969222] [doi: 10.1021/acs.jproteome.0c00536] [pdf]

  2. Njølstad PR$, Andreassen OA, Brunak S, Børglum AD, Dillner J, Esko T, Franks PW, Freimer N, Groop L, Heimer H, Hougaard DM, Hovig E, Hveem K, Jalanko A, Kaprio J, Knudsen GP, Melbye M, Metspalu A, Mortensen PB, Palmgren J, Palotie A, Reed W, Stefánsson H, Stitziel NO, Sullivan PF, Thorsteinsdóttir U, Vaudel M, Vuorio E, Werge T, Stoltenberg C, Stefánsson K. Roadmap for a precision-medicine initiative in the Nordic region, Nature Genetics, 2019. [PubMed id 30988515] [doi: 10.1038/s41588-019-0391-1] [No Open Access found Request a reprint]

  3. Grüning BA, Lampa S, Vaudel M, Blankenberg D$. Software engineering for scientific big data analysis, Gigascience, 2019. [PubMed id 31121028] [doi: 10.1093/gigascience/giz054] [pdf]

  4. Willems S, bouyssié D, Deforce D, Dorfer V, Gorshkov V, Kopczynski D, Laukens K, Locard-Paulet M, Schwämml V, Uszkoreit J, Valkenborg D, Vaudel M, Bittremieux W$. Proceedings of the EuBIC developer’s meeting 2018, Journal of Proteomics, 2018. [PubMed id 29864591] [doi: 10.1016/j.jprot.2018.05.015] [pdf]

  5. Willems S, Bouyssié D, David M, Locard-Paulet M, Mechtler K, Schwämmle V, Uszkoreit J, Vaudel M, Dorfer V$. Proceedings of the EuBIC Winter School 2017, Journal of Proteomics, 2017. [PubMed id 28385664] [doi: 10.1016/j.jprot.2017.04.001] [pdf]

  6. Guldbrandsen A, Vaudel M, Barsnes H$. Framtiden for biomedisinsk forskning - store endringer og nye muligheter, Best Practice Nordic, 2017. (Not peer reviewed) [PubMed] [no DOI yet] [pdf (accepted version)] [Request a reprint]

  7. Vaudel M, Veit Schwämmle$, Viktoria Dorfer. The EuPA Bioinformatics Community (EuBIC) initiative, EuPA Open Proteomics, 2016. [PubMed id] [doi: 10.1016/j.euprot.2016.03.009] [pdf]


Reviews

  1. Muth T$, Hartkopf F, Vaudel M$, Renard BY. A Potential Golden Age to Come-Current Tools, Recent Use Cases, and Future Avenues for De Novo Sequencing in Proteomics, Proteomics, 2018. [PubMed id 29968278] [doi: 10.1002/pmic.201700150] [pdf]

  2. Verheggen K, Ræder H, Breven FS, Martens L$, Barsnes H, Vaudel M. Anatomy and evolution of database search engines—a central component of mass spectrometry based proteomic workflows, Mass Spectrometry Reviews, 2017. [PubMed id 28902424] [doi: 10.1002/mas.21543] [No Open Access found Request a reprint]

  3. Hernandez-Valladares M$, Vaudel M, Selheim F, Berven F, Bruserud Ø. Proteogenomics approaches for studying cancer biology and their potential in the identification of Acute Myeloid Leukemia biomarkers, Expert Reviews of Proteomics, 2017. [PubMed id 28693350] [doi: 10.1080/14789450.2017.1352474] [No Open Access found Request a reprint]

  4. Vaudel M, Verheggen K, Csordas A, Raeder H, Berven FS, Martens L, Vizcaíno JA, Barsnes H$. Exploring the potential of public proteomics data, Proteomics, 2015. [PubMed id 26449181] [doi: 10.1002/pmic.201500295] [pdf]

  5. Vaudel M$, Barsnes H, Bjerkvig R, Bikfalvi A, Selheim F, Berven FS, Daubon T. Practical considerations for omics experiments in biomedical sciences, Current Pharmaceutical Biotechnology, 2015. [PubMed id 26278526] [doi: 10.2174/1389201016666150817095348] [pdf]

  6. Vaudel M$, Sickmann A, Martens L. Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics, Biochim Biophys Acta, 2014. [PubMed id 23845992] [doi: 10.1016/j.bbapap.2013.06.019] [pdf]

  7. Vaudel M, Sickmann A, Martens L$. Current methods for global proteome identification, Expert Reviews of Proteomics, 2012. [PubMed id 23194269] [doi: 10.1586/epr.12.51] [No Open Access found Request a reprint]

  8. Vaudel M$, Sickmann A, Martens L. Peptide and protein quantification: a map of the minefield, Proteomics, 2010. [PubMed id 19953549] [doi: 10.1002/pmic.200900481] [No Open Access found Request a reprint]


Book Chapters

Note: in our scientific field, book chapters are rarely peer reviewed by external experts and do not present substantial research advances.

  1. Vaudel M$. Proteomics, Processing Metabolomics and Proteomics Data with Open Software: A Practical Guide, 2019. [PubMed] [doi: 10.1039/9781788019880-00096] [No Open Access found Request a reprint]

  2. Schwämmle V$, Vaudel M. Computational and Statistical Methods for High-Throughput Mass Spectrometry-Based PTM Analysis, Methods in Molecular Biology: Protein Bioinformatics, Springer, 2017. [PubMed id 28150251] [doi: 10.1007/978-1-4939-6783-4_21] [No Open Access found Request a reprint]

  3. Vaudel M$. MS2-Based Quantitation, Proteome Informatics, Royal Society of Chemistry, 2016. [PubMed] [doi: 10.1039/9781782626732-00155] [No Open Access found Request a reprint]

  4. Lereim RR, Oveland E, Berven FS, Vaudel M$, Barsnes H. Visualization, Inspection and Interpretation of Shotgun Proteomics Identification Results, Advances in Experimental Medicine and Biology: Modern Proteomics – Sample Preparation, Analysis and Practical Applications, Springer, 2016. [PubMed id 27975220] [doi: 10.1007/978-3-319-41448-5_11] [No Open Access found Request a reprint]

  5. Muth T, Rapp E, Berven FS, Barsnes H, Vaudel M$. Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics, Advances in Experimental Medicine and Biology: Modern Proteomics – Sample Preparation, Analysis and Practical Applications, Springer, 2016. [PubMed id 27975219] [doi: 10.1007/978-3-319-41448-5_10] [No Open Access found Request a reprint]

  6. Verheggen K, Martens L, Berven FS, Barsnes H, Vaudel M$. Database Search Engines: Paradigms, Challenges and Solutions, Advances in Experimental Medicine and Biology: Modern Proteomics – Sample Preparation, Analysis and Practical Applications, Springer, 2016. [PubMed id 27975215] [doi: 10.1007/978-3-319-41448-5_6] [No Open Access found Request a reprint]

  7. Vaudel M$, Barsnes H, Ræder H, Berven FS. Using Proteomics Bioinformatics Tools and Resources in Proteogenomic Studies, Advances in Experimental Medicine and Biology: Proteogenomics, Springer, 2016. [PubMed id 27686806] [doi: 10.1007/978-3-319-42316-6_5] [No Open Access found Request a reprint]

  8. Hernández Sánchez LF, Aasebø E, Selheim F, Berven FS, Ræder H, Barsnes H, Vaudel M$. Systemic Analysis of Regulated Functional Networks, Methods in Molecular Biology: Proteomics in Systems Biology, Springer, 2015. [PubMed id 26700057] [doi: 10.1007/978-1-4939-3341-9_21] [No Open Access found Request a reprint]

  9. Guldbrandsen A, Barsnes H, Kroksveen AC, Berven FS, Vaudel M$. A Simple Workflow for Large Scale Shotgun Glycoproteomics, Methods in Molecular Biology: Proteomics in Systems Biology, Springer, 2015. [PubMed id 26700056] [doi: 10.1007/978-1-4939-3341-9_20] [No Open Access found Request a reprint]

  10. Aasebø E, Berven FS, Selheim F, Barsnes H, Vaudel M$. Interpretation of Quantitative Shotgun Proteomic Data, Methods in Molecular Biology: Proteomics in Systems Biology, Springer, 2015. [PubMed id 26700055] [doi: 10.1007/978-1-4939-3341-9_19] [No Open Access found Request a reprint]

  11. Vaudel M$, Barsnes H, Martens L, Berven FS. Bioinformatics for Proteomics: Opportunities at the interface between the scientists, their experiments and the community, Methods in Molecular Biology: Shotgun Proteomics, Springer, 2015. [PubMed id 24791993] [doi: 10.1007/978-1-4939-0685-7_16] [No Open Access found Request a reprint]

  12. Vaudel M1, Burkhart JM1, Zahedi RP, Martens L, Sickmann A$. iTRAQ data interpretation, Methods in Molecular Biology: Quantitative Methods in Proteomics, Springer, 2012. [PubMed id 22665319] [doi: 10.1007/978-1-61779-885-6_30] [pdf]


PhD thesis

Detailed analysis of the blood platelet proteome through the use of innovative bioinformatics methods for protein identification, quantification and post-translational modification localization, Ghent University, Faculty of Medicine and Health Sciences, 2012 (monograph). [link]


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R Session Info

sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=nb_NO.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=nb_NO.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=nb_NO.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] roadoi_0.7.2     conflicted_1.2.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.9       plyr_1.8.7       pillar_1.9.0     compiler_4.2.1  
##  [5] later_1.3.0      tools_4.2.1      digest_0.6.29    jsonlite_1.8.4  
##  [9] evaluate_0.16    memoise_2.0.1    lifecycle_1.0.3  tibble_3.2.1    
## [13] pkgconfig_2.0.3  rlang_1.1.1      shiny_1.7.2      cli_3.6.0       
## [17] rstudioapi_0.14  curl_4.3.2       yaml_2.3.5       xfun_0.33       
## [21] fastmap_1.1.0    dplyr_1.1.2      stringr_1.5.0    httr_1.4.5      
## [25] knitr_1.39       generics_0.1.3   vctrs_0.6.2      tidyselect_1.2.0
## [29] glue_1.6.2       R6_2.5.1         fansi_1.0.4      rmarkdown_2.15  
## [33] tidyr_1.3.0      purrr_1.0.1      magrittr_2.0.3   promises_1.2.0.1
## [37] htmltools_0.5.3  ellipsis_0.3.2   mime_0.12        xtable_1.8-4    
## [41] httpuv_1.6.5     utf8_1.2.3       stringi_1.7.8    miniUI_0.1.1.1  
## [45] cachem_1.0.6