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Research Output

2020
Open Access
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Gene Co-expression Network Analysis Associated with Acupuncture Treatment of Rheumatoid Arthritis: An Animal Model

Ravn, D., Mohammadnejad, A., Sabaredzovic, K., Li, W., Lund, J., Li, S., Svendsen, A. J., Schwämmle, V. & Tan, Q., 2020, In : Journal of Acupuncture Research. 37, 2, p. 128-135 8 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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7 Downloads (Pure)

JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools

Friedrichs, M., Shoshi, A., Chmura, P. J., Ison, J., Schwämmle, V., Schreiber, F., Hofestädt, R. & Sommer, B., 2020, In : Journal of Integrative Bioinformatics. 16, 4, 8 p., 20190059.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Middle-Down Proteomic Analyses with Ion Mobility Separations of Endogenous Isomeric Proteoforms

Shliaha, P. V., Gorshkov, V., Kovalchuk, S. I., Schwämmle, V., Baird, M. A., Shvartsburg, A. A. & Jensen, O. N., 2020, In : Analytical chemistry. 92, 3, p. 2364-2368

Research output: Contribution to journalJournal articleResearchpeer-review

Visualization of the dynamics of histone modifications and their crosstalk using PTM-CrossTalkMapper

Kirsch, R., Jensen, O. N. & Schwämmle, V., 21. Jan 2020, (Accepted/In press) In : Methods.

Research output: Contribution to journalJournal articleResearchpeer-review

A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation

Wong, J. E. M. M., Nadzieja, M., Madsen, L. H., Bücherl, C. A., Dam, S., Sandal, N. N., Couto, D., Derbyshire, P., Uldum-Berentsen, M., Schroeder, S., Schwämmle, V., Nogueira, F. C. S., Asmussen, M. H., Thirup, S., Radutoiu, S., Blaise, M., Andersen, K. R., Menke, F. L. H., Zipfel, C. & Stougaard, J., 25. Jun 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 28, p. 14339-14348 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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71 Downloads (Pure)

Automated workflow composition in mass spectrometry-based proteomics

Palmblad, M., Lamprecht, A-L., Ison, J. & Schwämmle, V., 15. Feb 2019, In : Bioinformatics (Oxford, England). 35, 4, p. 656–664

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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106 Downloads (Pure)

CoExpresso: Assess the quantitative behavior of protein complexes in human cells

Chalabi, M. H., Tsiamis, V., Käll, L., Vandin, F. & Schwämmle, V., 9. Jan 2019, In : BMC Bioinformatics. 20, 1, p. 1-10 17.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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135 Downloads (Pure)

Community curation of bioinformatics software and data resources

Ison, J., Ménager, H., Brancotte, B., Jaaniso, E., Salumets, A., Raček, T., Lamprecht, A-L., Palmblad, M., Kalaš, M., Chmura, P., Hancock, J. M., Schwämmle, V. & Ienasescu, H-I., 16. Oct 2019, In : Briefings in Bioinformatics.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2 Downloads (Pure)

ComplexBrowser: a tool for identification and quantification of protein complexes in large-scale proteomics datasets

Michalak, W., Tsiamis, V., Schwammle, V. & Rogowska-Wrzesinska, A., Nov 2019, In : Molecular and Cellular Proteomics. 18, 11, p. 2324-2334 12 p.

Research output: Contribution to journalJournal articleResearchpeer-review

IsoProt: A Complete and Reproducible Workflow to Analyze iTRAQ/TMT Experiments

Griss, J., Vinterhalter, G. & Schwämmle, V., 2019, In : Journal of Proteome Research. 18, 4, p. 1751-1759

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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148 Downloads (Pure)

One Thousand and One Software for Proteomics: Tales of the Toolmakers of Science

Tsiamis, V., Ienasescu, H. I., Gabrielaitis, D., Palmblad, M., Schwämmle, V. & Ison, J., 2019, In : Journal of Proteome Research. 18, 10, p. 3580-3585 6 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Proceedings of the EuBIC Winter School 2019

Kopczynski, D., Bittremieux, W., Bouyssié, D., Dorfer, V., Locard-Paulet, M., Van Puyvelde, B., Schwämmle, V., Soggiu, A., Willems, S. & Uszkoreit, J., Mar 2019, In : EuPA Open Proteomics. 22-23, p. 4-7 4 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Quantitative Proteomic Map of the Trypanosomatid Strigomonas culicis: The Biological Contribution of its Endosymbiotic Bacterium

Brunoro, G. V. F., Menna-Barreto, R. F. S., Garcia-Gomes, A. S., Boucinha, C., Lima, D. B., Carvalho, P. C., Teixeira-Ferreira, A., Trugilho, M. R. O., Perales, J., Schwämmle, V., Catanho, M., de Vasconcelos, A. T. R., Motta, M. C. M., d'Avila-Levy, C. M. & Valente, R. H., Dec 2019, In : Protist. 170, 6, 21 p., 125698.

Research output: Contribution to journalJournal articleResearchpeer-review

The bio.tools registry of software tools and data resources for the life sciences

Ison, J., Ienasescu, H., Chmura, P., Rydza, E., Menager, H., Kalaš, M., Schwammle, V., Gruning, B., Beard, N., Lopez, R., Duvaud, S., Stockinger, H., Persson, B., Vařekova, R. S., Raček, T., Vondrašek, J., Peterson, H., Salumets, A., Jonassen, I., Hooft, R. & 16 others, Nyronen, T., Valencia, A., Capella, S., Gelpi, J., Zambelli, F., Savakis, B., Leskošek, B., Rapacki, K., Blanchet, C., Jimenez, R., Oliveira, A., Vriend, G., Collin, O., Van Helden, J., Løngreen, P. & Brunak, S., Aug 2019, In : Genome Biology. 20, 1, 4 p., 164.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2018

Analysis of the effect of intestinal ischemia and reperfusion on the rat neutrophils proteome

Tahir, M., Arshid, S., Fontes, B., Castro, M. S., Luz, I. S., Botelho, K. L. R., Sidoli, S., Schwämmle, V., Roepstorff, P. & Fontes, W., 29. Nov 2018, In : Frontiers in Molecular Biosciences. 5, p. 1-15 89.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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115 Downloads (Pure)

Automated composition of scientific workflows in mass spectrometry-based proteomics

Lamprecht, A. L., Palmblad, M., Ison, J. & Schwammle, V., 27. Dec 2018, Proceedings - IEEE 14th International Conference on eScience, e-Science 2018. IEEE, p. 360-361

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Distinct urinary glycoprotein signatures in prostate cancer patients

Kawahara, R., Ortega, F., Rosa-Fernandes, L., Guimarães, V., Quina, D., Nahas, W., Schwämmle, V., Srougi, M., Leite, K. R. M., Thaysen-Andersen, M., Larsen, M. R. & Palmisano, G., 4. Sep 2018, In : Oncotarget. 9, 69, p. 33077-33097

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy

Greer, S. M., Sidoli, S., Coradin, M., Schack Jespersen, M., Schwämmle, V., Jensen, O. N., Garcia, B. A. & Brodbelt, J. S., Sep 2018, In : Analytical Chemistry. 90, 17, p. 10425–10433

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Maximizing Sequence Coverage in Top-Down Proteomics By Automated Multi-modal Gas-phase Protein Fragmentation

Shliaha, P. V., Gibb, S., Gorshkov, V., Jespersen, M. S., Andersen, G. R., Bailey, D., Schwartz, J., Eliuk, S., Schwämmle, V. & Jensen, O. N., 25. Sep 2018, In : Analytical Chemistry. 90, 21, p. 12519-12526

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Proceedings of the EuBIC developer's meeting 2018

Willems, S., Bouyssié, D., Deforce, D., Dorfer, V., Gorshkov, V., Kopczynski, D., Laukens, K., Locard-Paulet, M., Schwämmle, V., Uszkoreit, J., Valkenborg, D., Vaudel, M. & Bittremieux, W., 15. Sep 2018, In : Journal of Proteomics. 187, p. 25-27

Research output: Contribution to journalJournal articleResearch

ProForma: A Standard Proteoform Notation

LeDuc, R. D., Schwämmle, V., Shortreed, M. R., Cesnik, A. J., Solntsev, S. K., Shaw, J. B., Martin, M. J., Vizcaino, J. A., Alpi, E., Danis, P., Kelleher, N. L., Smith, L. M., Ge, Y., Agar, J. N., Chamot-Rooke, J., Loo, J. A., Pasa-Tolic, L. & Tsybin, Y. O., 2018, In : Journal of Proteome Research. 17, 3, p. 1321-1325

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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198 Downloads (Pure)

VSClust: Feature-based variance-sensitive clustering of omics data

Schwämmle, V. & Jensen, O. N., Sep 2018, In : Bioinformatics. 34, 17, p. 2965–2972

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2017

Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape

Tvardovskiy, A., Schwämmle, V., Kempf, S. J., Rogowska-Wrzesinska, A. & Jensen, O. N., 2017, In : Nucleic Acids Research. 45, 16, p. 9272-9289

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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236 Downloads (Pure)

A community proposal to integrate proteomics activities in ELIXIR

Vizcaíno, J. A., Walzer, M., Jiménez, R. C., Bittremieux, W., Bouyssié, D., Carapito, C., Corrales, F., Ferro, M., Heck, A. J. R., Horvatovich, P., Hubalek, M., Lane, L., Laukens, K., Levander, F., Lisacek, F., Novak, P., Palmblad, M., Piovesan, D., Pühler, A., Schwämmle, V. & 6 others, Valkenborg, D., van Rijswijk, M., Vondrasek, J., Eisenacher, M., Martens, L. & Kohlbacher, O., 2017, In : F1000Research. 6, 11 p., 875.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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194 Downloads (Pure)

Computational and statistical methods for high-throughput mass spectrometry-based PTM analysis

Schwämmle, V. & Vaudel, M., 2017, Protein Bioinformatics. H. Wu, C., N. Arighi, C. & E. Ross, K. (eds.). Humana Press, p. 437-458 (Methods in Molecular Biology, Vol. 1558).

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

Neutrophil proteomic analysis reveals the participation of antioxidant enzymes, motility and ribosomal proteins in the prevention of ischemic effects by preconditioning

Arshid, S., Tahir, M., Fontes, B., Montero, E. F. S., Castro, M. S., Sidoli, S., Schwämmle, V., Roepstorff, P. & Fontes, W., 2017, In : Journal of Proteomics. 151, p. 162-173

Research output: Contribution to journalJournal articleResearchpeer-review

Nuclear phosphoproteome analysis of 3T3-L1 preadipocyte differentiation reveals system-wide phosphorylation of transcriptional regulators

Rabiee, A., Schwämmle, V., Sidoli, S., Dai, J., Rogowska-Wrzesinska, A., Mandrup, S. & Jensen, O. N., 2017, In : Proteomics. 17, 6, 5 p., 1600248.

Research output: Contribution to journalJournal articleResearchpeer-review

Proceedings of the EuBIC Winter School 2017

Willems, S., Bouyssié, D., David, M., Locard-Paulet, M., Mechtler, K., Schwämmle, V., Uszkoreit, J., Vaudel, M. & Dorfer, V., 2017, In : Journal of Proteomics. 161, p. 78-80

Research output: Contribution to journalJournal articleCommunication

2016

High-performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis: Observations and implications

Williamson, J. C., Edwards, A. V. G., Verano-Braga, T., Schwämmle, V., Kjeldsen, F., Jensen, O. N. & Larsen, M. R., Mar 2016, In : Proteomics. 16, 6, p. 907-914

Research output: Contribution to journalJournal articleResearchpeer-review

Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation

Schwämmle, V., Sidoli, S., Ruminowicz, C., Wu, X., Lee, C-F., Helin, K. & Jensen, O. N., 2016, In : Molecular and Cellular Proteomics. 15, 8, p. 2715-2729

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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Tools and data services registry: a community effort to document bioinformatics resources

Ison, J., Rapacki, K., Ménager, H., Kalaš, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., Vedova, G. D. & 49 others, Dogan, T., Doppelt-Azeroual, O., Emery, L., Gasteiger, E., Gatter, T., Goldberg, T., Grosjean, M., Grüning, B., Helmer-Citterich, M., Ienasescu, H., Ioannidis, V., Jespersen, M. C., Jimenez, R., Juty, N., Juvan, P., Koch, M., Laibe, C., Li, J-W., Licata, L., Mareuil, F., Mičetić, I., Friborg, R. M., Moretti, S., Morris, C., Möller, S., Nenadic, A., Peterson, H., Profiti, G., Rice, P., Romano, P., Roncaglia, P., Saidi, R., Schafferhans, A., Schwämmle, V., Smith, C., Sperotto, M. M., Stockinger, H., Vařeková, R. S., Tosatto, S. C. E., de la Torre, V., Uva, P., Via, A., Yachdav, G., Zambelli, F., Vriend, G., Rost, B., Parkinson, H., Løngreen, P. & Brunak, S., 2016, In : Nucleic Acids Research. 44, p. D38–D47

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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2015

Computational and statistical methods for high-throughput analysis of post-translational modifications of proteins

Schwämmle, V., Braga, T. V. & Roepstorff, P., 2015, In : Journal of Proteomics. 129, p. 3-15

Research output: Contribution to journalReviewResearchpeer-review

2014

Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk

Schwämmle, V., Aspalter, C-M., Sidoli, S. & Jensen, O. N., Jul 2014, In : Molecular & Cellular Proteomics. 13, 7, p. 1855-65 11 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones

Sidoli, S., Schwämmle, V., Ruminowicz, C., Hansen, T. A., Wu, X., Helin, K. & Jensen, O. N., Oct 2014, In : Proteomics. 14, 19, p. 2200-11 12 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Neuronal process structure and growth proteins are targets of heavy PTM regulation during brain development

Edwards, A. V. G., Schwämmle, V. & Larsen, M. R., 14. Apr 2014, In : Journal of Proteomics. 101, p. 77-87

Research output: Contribution to journalJournal articleResearchpeer-review

Quantitative Proteomic and Phosphoproteomic Analysis of Trypanosoma cruzi Amastigogenesis

Queiroz, R. M. L., Charneau, S., Mandacaru, S. C., Schwämmle, V., Lima, B. D., Roepstorff, P. & Ricart, C. A. O., 15. Sep 2014, In : Molecular & Cellular Proteomics. 13, 12, p. 3457-3472

Research output: Contribution to journalJournal articleResearchpeer-review

Selective renal vasoconstriction, exaggerated natriuresis and excretion rates of exosomic proteins in essential hypertension

Damkjaer, M., Jensen, P. H., Schwämmle, V., Sprenger, R. R., Jacobsen, I. A., Jensen, O. N. & Bie, P., Sep 2014, In : Acta Physiologica. 212, 1, p. 106-118 13 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Spatial and Temporal Effects in Protein Post-translational Modification Distributions in the Developing Mouse Brain

Edwards, A. V. G., Edwards, G. J., Schwämmle, V., Saxtorph, H. & Larsen, M. R., 2014, In : Journal of Proteome Research. 13, 1, p. 260–267

Research output: Contribution to journalJournal articleResearchpeer-review

The Cultural Divide: Exponential Growth in Classical 2D and Metabolic Equilibrium in 3D Environments

Wrzesinski, K., Rogowska-Wrzesinska, A., Kanlaya, R., Borkowski, K., Schwämmle, V., Joensen, K., Wojdyla, K. I., Carvalho, V. B. & Fey, S. J., 15. Sep 2014, In : P L o S One. 9, 9, p. 1 - 15 15 p., e106973.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
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496 Downloads (Pure)
2013

A Computational Model for Histone Mark Propagation Reproduces the Distribution of Heterochromatin in Different Human Cell Types

Schwämmle, V. & Jensen, O. N., 2013, In : P L o S One. 8, 9, p. e73818 e73818.

Research output: Contribution to journalJournal articleResearchpeer-review

A proteomics approach to the identification of biomarkers for psoriasis utilising keratome biopsy

Williamson, J. C., Scheipers, P., Schwämmle, V., Zibert, J. R., Beck, H. C. & Jensen, O. N., 2013, In : Journal of Proteomics. 94, p. 176-185

Research output: Contribution to journalJournal articleResearchpeer-review

Assessment and improvement of statistical tools for comparative proteomics analysis of sparse data sets with few experimental replicates

Schwämmle, V., León, I. R. & Jensen, O. N., 2013, In : Journal of Proteome Research. 12, 9, p. 3874-3883

Research output: Contribution to journalJournal articleResearchpeer-review

Evolving cellular automata for diversity generation and pattern recognition: deterministic versus random strategy

de Menezes, M. A., Brigatti, E. & Schwämmle, V., 2013, In : Journal of Statistical Mechanics: Theory and Experiment. 2013, 8, 13 p., P08006.

Research output: Contribution to journalJournal articleResearchpeer-review

Isotope labeling-based quantitative proteomics of developing seeds of castor oil seed (Ricinus communis L.)

Nogueira, F. C. S., Palmisano, G., Schwämmle, V., Soares, E. L., Soares, A. A., Roepstorff, P., Domont, G. B. & Campos, F. A. P., 2013, In : Journal of Proteome Research. 12, 11, p. 5012-24

Research output: Contribution to journalJournal articleResearchpeer-review

Precision mapping of coexisting modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS

Jung, H. R., Sidoli, S., Haldbo, S., Sprenger, R. R., Schwämmle, V., Pasini, D., Helin, K. & Jensen, O. N., 2013, In : Analytical Chemistry. 85, 17, p. 8232–8239

Research output: Contribution to journalJournal articleResearchpeer-review

2012

A novel method for the simultaneous enrichment, identification and quantification of phosphopeptides and sialyted glycopeptides applied to a temporal profile of mouse brain development

Palmisano, G., Parker, B., Engholm-Keller, K., Lendal, S. E., Kulej, K., Schulz, M., Schwämmle, V., Graham, M. E., Saxtorph, H., Cordwell, S. & Larsen, M. R., 2012, In : Molecular and Cellular Proteomics. 11, 11, p. 1191-1202

Research output: Contribution to journalJournal articleResearchpeer-review