Research output per year
Research output per year
- 1 - 50 out of 82 results
Search results
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2025
Alternative Splicing in Mechanically Stretched Podocytes as a Model of Glomerular Hypertension
Mattias, F., Tsoy, O., Hammer, E., Gress, A., Simm, S., Lio, C. T., Ameling, S., Amann, K., Dreher, L., Wenzel, U., Kacprowski, T., List, M., Kalinina, O., Endlich, K., Baumbach, J., Völker, U., Endlich, N. & Kliewe, F., 2025, (Accepted/In press) In: Journal of the American Society of Nephrology. 10.1681/ASN.0000000706.Research output: Contribution to journal › Article › peer-review
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Next-generation deconvolution of the tumor microenvironment with omnideconv
Merotto, L., Dietrich, A., List, M. & Finotello, F., 2025, (Accepted/In press) Methods in Cell Biology. Academic Press Inc., (Methods in Cell Biology).Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review
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Persistent desmoglein-1 downregulation and periostin accumulation in histologic remission of eosinophilic esophagitis
Hoelz, H., Faro, T., Frank, M. L., Forné, I., Kugelmann, D., Jurk, A., Buehler, S., Siebert, K., Matchado, M., Straub, T., Hering, A., Piontek, G., Mueller, S., Koletzko, S., List, M., Steiger, K., Rudelius, M., Waschke, J. & Schwerd, T., Feb 2025, In: Journal of Allergy and Clinical Immunology. 155, 2, p. 505-519 15 p.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
Systematic evaluation of normalization approaches in tandem mass tag and label-free protein quantification data using PRONE
Arend, L., Adamowicz, K., Schmidt, J. R., Burankova, Y., Zolotareva, O., Tsoy, O., Pauling, J. K., Kalkhof, S., Baumbach, J., List, M. & Laske, T., 1 May 2025, In: Briefings in Bioinformatics. 26, 3, bbaf201.Research output: Contribution to journal › Article › peer-review
Open Access -
2024
AI in microbiome-related healthcare
Probul, N., Huang, Z., Saak, C. C., Baumbach, J. & List, M., Nov 2024, In: Microbial Biotechnology. 17, 11, e70027.Research output: Contribution to journal › Short survey › peer-review
Open Access3 Scopus citations -
Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2
Hoffmann, M., Willruth, L. L., Dietrich, A., Lee, H. K., Knabl, L., Trummer, N., Baumbach, J., Furth, P. A., Hennighausen, L. & List, M., Dec 2024, In: Scientific Reports. 14, 1, 2808.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Diurnal rhythmicity of infant fecal microbiota and metabolites: A randomized controlled interventional trial with infant formula
Heppner, N., Reitmeier, S., Heddes, M., Merino, M. V., Schwartz, L., Dietrich, A., List, M., Gigl, M., Meng, C., van der Veen, D. R., Schirmer, M., Kleigrewe, K., Omer, H., Kiessling, S. & Haller, D., 10 Apr 2024, In: Cell Host and Microbe. 32, 4, p. 573-587.e5Research output: Contribution to journal › Article › peer-review
Open Access13 Scopus citations -
Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing
Maier, A., Hartung, M., Abovsky, M., Adamowicz, K., Bader, G. D., Baier, S., Blumenthal, D. B., Chen, J., Elkjaer, M. L., Garcia-Hernandez, C., Helmy, M., Hoffmann, M., Jurisica, I., Kotlyar, M., Lazareva, O., Levi, H., List, M., Lobentanzer, S., Loscalzo, J. & Malod-Dognin, N. & 20 others, , 5 Jul 2024, In: Nucleic Acids Research. 52, W1, p. W481-W488Research output: Contribution to journal › Article › peer-review
10 Scopus citations -
DysRegNet: Patient-specific and confounder-aware dysregulated network inference towards precision therapeutics
Kersting, J., Lazareva, O., Louadi, Z., Baumbach, J., Blumenthal, D. B. & List, M., 2024, (Accepted/In press) In: British Journal of Pharmacology.Research output: Contribution to journal › Article › peer-review
Open Access -
Emergence of power law distributions in protein-protein interaction networks through study bias
Blumenthal, D. B., Lucchetta, M., Kleist, L., Fekete, S. P., List, M. & Schaefer, M. H., 11 Dec 2024, In: eLife. 13Research output: Contribution to journal › Article › peer-review
Open Access -
Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease
Häcker, D., Siebert, K., Smith, B. J., Köhler, N., Riva, A., Mahapatra, A., Heimes, H., Nie, J., Metwaly, A., Hölz, H., Manz, Q., De Zen, F., Heetmeyer, J., Socas, K., Le Thi, G., Meng, C., Kleigrewe, K., Pauling, J. K., Neuhaus, K. & List, M. & 3 others, , 13 Nov 2024, In: Cell Host and Microbe. 32, 11, p. 2019-2034.e8Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Inference of differential gene regulatory networks using boosted differential trees
Galindez, G., List, M., Baumbach, J., Völker, U., Mäder, U., Blumenthal, D. B. & Kacprowski, T., 2024, In: Bioinformatics Advances. 4, 1, vbae034.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
Making mouse transcriptomics deconvolution accessible with immunedeconv
Merotto, L., Sturm, G., Dietrich, A., List, M. & Finotello, F., 2024, In: Bioinformatics Advances. 4, 1, vbae032.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Meta-analysis of proteomics data from osteoblasts, bone, and blood: Insights into druggable targets, active factors, and potential biomarkers for bone biomaterial design
Schmidt, J. R., Adamowicz, K., Arend, L., Lehmann, J., List, M., Poh, P. S. P., Baumbach, J., Kalkhof, S. & Laske, T., 1 Jan 2024, In: Journal of Tissue Engineering. 15Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
MeTEor: an R Shiny app for exploring longitudinal metabolomics data
Grabert, G., Dehncke, D., More, T., List, M., Kraft, A. R. M., Cornberg, M., Hiller, K. & Kacprowski, T., 2024, In: Bioinformatics Advances. 4, 1, vbae178.Research output: Contribution to journal › Article › peer-review
Open Access -
Mitochondrial perturbation in the intestine causes microbiota-dependent injury and gene signatures discriminative of inflammatory disease
Urbauer, E., Aguanno, D., Mindermann, N., Omer, H., Metwaly, A., Krammel, T., Faro, T., Remke, M., Reitmeier, S., Bärthel, S., Kersting, J., Huang, Z., Xian, F., Schmidt, M., Saur, D., Huber, S., Stecher, B., List, M., Gómez-Varela, D. & Steiger, K. & 3 others, , 14 Aug 2024, In: Cell Host and Microbe. 32, 8, p. 1347-1364.e10Research output: Contribution to journal › Article › peer-review
4 Scopus citations -
Network medicine-based epistasis detection in complex diseases: Ready for quantum computing
Hoffmann, M., Poschenrieder, J. M., Incudini, M., Baier, S., Fritz, A., Maier, A., Hartung, M., Hoffmann, C., Trummer, N., Adamowicz, K., Picciani, M., Scheibling, E., Harl, M. V., Lesch, I., Frey, H., Kayser, S., Wissenberg, P., Schwartz, L., Hafner, L. & Acharya, A. & 28 others, , 23 Sep 2024, In: Nucleic Acids Research. 52, 17, p. 10144-10160 17 p.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling
Matchado, M. S., Rühlemann, M., Reitmeier, S., Kacprowski, T., Frost, F., Haller, D., Baumbach, J. & List, M., 1 Feb 2024, In: Microbial Genomics. 10, 2, 001203.Research output: Contribution to journal › Article › peer-review
Open Access37 Scopus citations -
Platelet mass cytometry reveals dysregulation of prothrombotic pathways in essential thrombocythemia
Dill, V., Kirmes, K., Han, J., Klug, M., Rosenbaum, M., Viggiani, G., von Scheidt, M., List, M., Herhaus, P., Ruland, J., Bassermann, F., Laugwitz, K. L., Götze, K. S., Jost, P. J., Jilg, S., Bloxham, C. J., Raake, P. W. J., Bernlochner, I. & Bongiovanni, D., 2024, In: Platelets. 35, 1, 2358244.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Single-cell transcriptome analysis reveals secretin as a hallmark of human enteroendocrine cell maturation
Hysenaj, F., Lauber, M., Bast-Habersbrunner, A., List, M. & Klingenspor, M., Dec 2024, In: Scientific Reports. 14, 1, 13525.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
2023
Alternative splicing analysis benchmark with DICAST
Fenn, A., Tsoy, O., Faro, T., Rößler, F. L. M., Dietrich, A., Kersting, J., Louadi, Z., Lio, C. T., Völker, U., Baumbach, J., Kacprowski, T. & List, M., 1 Jun 2023, In: NAR Genomics and Bioinformatics. 5, 2, lqad044.Research output: Contribution to journal › Article › peer-review
Open Access8 Scopus citations -
Alternative splicing impacts microRNA regulation within coding regions
Hackl, L. M., Fenn, A., Louadi, Z., Baumbach, J., Kacprowski, T., List, M. & Tsoy, O., 1 Sep 2023, In: NAR Genomics and Bioinformatics. 5, 3, lqad081.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
CircRNA-sponging: A pipeline for extensive analysis of circRNA expression and their role in miRNA sponging
Hoffmann, M., Schwartz, L., Ciora, O. A., Trummer, N., Willruth, L. L., Jankowski, J., Lee, H. K., Baumbach, J., Furth, P. A., Hennighausen, L. & List, M., 2023, In: Bioinformatics Advances. 3, 1, vbad093.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Computational tools for inferring transcription factor activity
Hecker, D., Lauber, M., Behjati Ardakani, F., Ashrafiyan, S., Manz, Q., Kersting, J., Hoffmann, M., Schulz, M. H. & List, M., Dec 2023, In: Proteomics. 23, 23-24, 2200462.Research output: Contribution to journal › Review article › peer-review
Open Access9 Scopus citations -
F-Prioritizer: A Java pipeline to prioritize condition-specific transcription factors
Hoffmann, M., Trummer, N., Schwartz, L., Jankowski, J., Lee, H. K., Willruth, L. L., Lazareva, O., Yuan, K., Baumgarten, N., Schmidt, F., Baumbach, J., Schulz, M. H., Blumenthal, D. B., Hennighausen, L. & List, M., 2023, In: GigaScience. 12, giad026.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Multi-omics regulatory network inference in the presence of missing data
Henao, J. D., Lauber, M., Azevedo, M., Grekova, A., Theis, F., List, M., Ogris, C. & Schubert, B., 1 Sep 2023, In: Briefings in Bioinformatics. 24, 5, bbad309.Research output: Contribution to journal › Article › peer-review
Open Access4 Scopus citations -
Network-based approaches for modeling disease regulation and progression
Galindez, G., Sadegh, S., Baumbach, J., Kacprowski, T. & List, M., Jan 2023, In: Computational and Structural Biotechnology Journal. 21, p. 780-795 16 p.Research output: Contribution to journal › Review article › peer-review
Open Access24 Scopus citations -
Online bias-aware disease module mining with ROBUST-Web
Sarkar, S., Lucchetta, M., Maier, A., Abdrabbou, M. M., Baumbach, J., List, M., Schaefer, M. H. & Blumenthal, D. B., 1 Jun 2023, In: Bioinformatics. 35, 6, btad345.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
SpongEffects: CeRNA modules offer patient-specific insights into the miRNA regulatory landscape
Boniolo, F., Hoffmann, M., Roggendorf, N., Tercan, B., Baumbach, J., Castro, M. A. A., Robertson, A. G., Saur, D. & List, M., 1 May 2023, In: Bioinformatics. 39, 5, btad276.Research output: Contribution to journal › Article › peer-review
Open Access9 Scopus citations -
Systematic analysis of alternative splicing in time course data using Spycone
Lio, C. T., Grabert, G., Louadi, Z., Fenn, A., Baumbach, J., Kacprowski, T., List, M. & Tsoy, O., 1 Jan 2023, In: Bioinformatics. 39, 1, btac846.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
The FeatureCloud Platform for Federated Learning in Biomedicine: Unified Approach
Matschinske, J., Späth, J., Bakhtiari, M., Probul, N., Majdabadi, M. M. K., Nasirigerdeh, R., Torkzadehmahani, R., Hartebrodt, A., Orban, B. A., Fejér, S. J., Zolotareva, O., Das, S., Baumbach, L., Pauling, J. K., Tomašević, O., Bihari, B., Bloice, M., Donner, N. C., Fdhila, W. & Frisch, T. & 19 others, , 2023, In: Journal of Medical Internet Research. 25, e42621.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
2022
Cancer driver drug interaction explorer
Hartung, M., Anastasi, E., Mamdouh, Z. M., Nogales, C., Schmidt, H. H. H. W., Baumbach, J., Zolotareva, O. & List, M., 5 Jul 2022, In: Nucleic Acids Research. 50, W1, p. W138-W144Research output: Contribution to journal › Article › peer-review
Open Access18 Scopus citations -
Gut Microbial Disruption in Critically Ill Patients with COVID-19-Associated Pulmonary Aspergillosis
Maurer, H. C., Schult, D., Koyumdzhieva, P., Reitmeier, S., Middelhoff, M., Rasch, S., List, M., Janssen, K. P., Steiger, K., Protzer, U., Schmid, R. M., Neuhaus, K., Haller, D., Quante, M. & Lahmer, T., Dec 2022, In: Journal of Fungi. 8, 12, 1265.Research output: Contribution to journal › Article › peer-review
Open Access2 Scopus citations -
KeyPathwayMineR: De Novo Pathway Enrichment in the R Ecosystem
Mechteridis, K., Lauber, M., Baumbach, J. & List, M., 31 Jan 2022, In: Frontiers in Genetics. 12, 812853.Research output: Contribution to journal › Article › peer-review
Open Access6 Scopus citations -
Mass cytometry of platelet-rich plasma: a new approach to analyze platelet surface expression and reactivity
Klug, M., Kirmes, K., Han, J., Lazareva, O., Rosenbaum, M., Viggiani, G., von Scheidt, M., Ruland, J., Baumbach, J., Condorelli, G., Laugwitz, K. L., List, M., Bernlochner, I. & Bongiovanni, D., 2022, In: Platelets. 33, 6, p. 841-848 8 p.Research output: Contribution to journal › Article › peer-review
5 Scopus citations -
Namco: a microbiome explorer
Dietrich, A., Matchado, M. S., Zwiebel, M., Ölke, B., Lauber, M., Lagkouvardos, I., Baumbach, J., Haller, D., Brandl, B., Skurk, T., Hauner, H., Reitmeier, S. & List, M., 2022, In: Microbial Genomics. 8, 8, 000852.Research output: Contribution to journal › Article › peer-review
Open Access15 Scopus citations -
Network pharmacology: curing causal mechanisms instead of treating symptoms
Nogales, C., Mamdouh, Z. M., List, M., Kiel, C., Casas, A. I. & Schmidt, H. H. H. W., Feb 2022, In: Trends in Pharmacological Sciences. 43, 2, p. 136-150 15 p.Research output: Contribution to journal › Review article › peer-review
Open Access691 Scopus citations -
Not Quite the Same: How Alternative Splicing Affects Protein Interactions
Louadi, Z., Tsoy, O., Baumbach, J., Kacprowski, T. & List, M., 1 Jan 2022, Protein Interactions: The Molecular Basis of Interactomics. wiley, p. 359-379 21 p.Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review
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On the limits of graph neural networks for the early diagnosis of Alzheimer’s disease
Hernández-Lorenzo, L., Hoffmann, M., Scheibling, E., List, M., Matías-Guiu, J. A. & Ayala, J. L., Dec 2022, In: Scientific Reports. 12, 1, 17632.Research output: Contribution to journal › Article › peer-review
Open Access16 Scopus citations -
Platelet Surface Protein Expression and Reactivity upon TRAP Stimulation after BNT162b2 Vaccination
Klug, M., Lazareva, O., Kirmes, K., Rosenbaum, M., Lukas, M., Weidlich, S., Spinner, C. D., Von Scheidt, M., Gosetti, R., Baumbach, J., Ruland, J., Condorelli, G., Laugwitz, K. L., List, M., Bernlochner, I. & Bongiovanni, D., 1 Oct 2022, In: Thrombosis and Haemostasis. 122, 10, p. 1706-1711 6 p.Research output: Contribution to journal › Article › peer-review
Open Access10 Scopus citations -
Privacy-Preserving Artificial Intelligence Techniques in Biomedicine
Torkzadehmahani, R., Nasirigerdeh, R., Blumenthal, D. B., Kacprowski, T., List, M., Matschinske, J., Spaeth, J., Wenke, N. K. & Baumbach, J., 1 Jun 2022, In: Methods of Information in Medicine. 61, p. E12-E27Research output: Contribution to journal › Article › peer-review
Open Access46 Scopus citations -
SimBu: Bias-Aware simulation of bulk RNA-seq data with variable cell-Type composition
Dietrich, A., Sturm, G., Merotto, L., Marini, F., Finotello, F. & List, M., 1 Sep 2022, In: Bioinformatics. 38, p. II141-II147Research output: Contribution to journal › Article › peer-review
Open Access12 Scopus citations -
The limits of molecular signatures for pancreatic ductal adenocarcinoma subtyping
Lautizi, M., Baumbach, J., Weichert, W., Steiger, K., List, M., Pfarr, N. & Kacprowski, T., 1 Dec 2022, In: NAR Cancer. 4, 4, zcac030.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
Un-biased housekeeping gene panel selection for high-validity gene expression analysis
Casas, A. I., Hassan, A. A., Manz, Q., Wiwie, C., Kleikers, P., Egea, J., López, M. G., List, M., Baumbach, J. & Schmidt, H. H. H. W., Dec 2022, In: Scientific Reports. 12, 1, 12324.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
2021
A framework for modeling epistatic interaction
Blumenthal, D. B., Baumbach, J., Hoffmann, M., Kacprowski, T. & List, M., 15 Jun 2021, In: Bioinformatics. 37, 12, p. 1708-1716 9 p.Research output: Contribution to journal › Article › peer-review
6 Scopus citations -
ASimulatoR: splice-aware RNA-Seq data simulation
Manz, Q., Tsoy, O., Fenn, A., Baumbach, J., Völker, U., List, M. & Kacprowski, T., 15 Sep 2021, In: Bioinformatics. 37, 18, p. 3008-3010 3 p.Research output: Contribution to journal › Article › peer-review
7 Scopus citations -
BiCoN: Network-constrained biclustering of patients and omics data
Lazareva, O., Canzar, S., Yuan, K., Baumbach, J., Blumenthal, D. B., Tieri, P., Kacprowski, T. & List, M., 15 Aug 2021, In: Bioinformatics. 37, 16, p. 2398-2404 7 p.Research output: Contribution to journal › Article › peer-review
Open Access21 Scopus citations -
Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside
on behalf of the International Network Medicine Consortium, Dec 2021, In: Clinical Epigenetics. 13, 1, 66.Research output: Contribution to journal › Review article › peer-review
Open Access54 Scopus citations -
Computational strategies to combat COVID-19: Useful tools to accelerate SARS-CoV-2 and coronavirus research
Hufsky, F., Lamkiewicz, K., Almeida, A., Aouacheria, A., Arighi, C., Bateman, A., Baumbach, J., Beerenwinkel, N., Brandt, C., Cacciabue, M., Chuguransky, S., Drechsel, O., Finn, R. D., Fritz, A., Fuchs, S., Hattab, G., Hauschild, A. C., Heider, D., Hoffmann, M. & Hölzer, M. & 35 others, , 1 Mar 2021, In: Briefings in Bioinformatics. 22, 2, p. 642-663 22 p.Research output: Contribution to journal › Review article › peer-review
Open Access113 Scopus citations -
DIGGER: Exploring the functional role of alternative splicing in protein interactions
Louadi, Z., Yuan, K., Gress, A., Tsoy, O., Kalinina, O. V., Baumbach, J., Kacprowski, T. & List, M., 8 Jan 2021, In: Nucleic Acids Research. 49, D1, p. D309-D318Research output: Contribution to journal › Article › peer-review
Open Access30 Scopus citations