Works matching AU List, Markus

Results: 57

DeepBlueR: large-scale epigenomic analysis in R.

Published in:

Bioinformatics, 2017, v. 33, n. 13, p. 2063, doi. 10.1093/bioinformatics/btx099

By:

Albrecht, Felipe;
List, Markus;
Bock, Christoph;
Lengauer, Thomas

Publication type:

Article

Microarray R-based analysis of complex lysate experiments with MIRACLE.

Published in:

Bioinformatics, 2014, v. 30, n. 17, p. i631, doi. 10.1093/bioinformatics/btu473

By:

List, Markus;
Block, Ines;
Pedersen, Marlene Lemvig;
Christiansen, Helle;
Schmidt, Steffen;
Thomassen, Mads;
Tan, Qihua;
Baumbach, Jan;
Mollenhauer, Jan

Publication type:

Article

BALSAM—An Interactive Online Platform for Breath Analysis, Visualization and Classification.

Published in:

Metabolites (2218-1989), 2020, v. 10, n. 10, p. 393, doi. 10.3390/metabo10100393

By:

Weber, Philipp;
Pauling, Josch Konstantin;
List, Markus;
Baumbach, Jan

Publication type:

Article

SARS-CoV-2 infection is associated with a pro-thrombotic platelet phenotype.

Published in:

Cell Death & Disease, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41419-020-03333-9

By:

Bongiovanni, Dario;
Klug, Melissa;
Lazareva, Olga;
Weidlich, Simon;
Biasi, Marina;
Ursu, Simona;
Warth, Sarah;
Buske, Christian;
Lukas, Marina;
Spinner, Christoph D.;
Scheidt, Moritz von;
Condorelli, Gianluigi;
Baumbach, Jan;
Laugwitz, Karl-Ludwig;
List, Markus;
Bernlochner, Isabell

Publication type:

Article

Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02538-1

By:

Louadi, Zakaria;
Elkjaer, Maria L.;
Klug, Melissa;
Lio, Chit Tong;
Fenn, Amit;
Illes, Zsolt;
Bongiovanni, Dario;
Baumbach, Jan;
Kacprowski, Tim;
List, Markus;
Tsoy, Olga

Publication type:

Article

AI in microbiome‐related healthcare.

Published in:

Microbial Biotechnology, 2024, v. 17, n. 11, p. 1, doi. 10.1111/1751-7915.70027

By:

Probul, Niklas;
Huang, Zihua;
Saak, Christina Caroline;
Baumbach, Jan;
List, Markus

Publication type:

Article

Computational tools for inferring transcription factor activity.

Published in:

Proteomics, 2023, v. 23, n. 23/24, p. 1, doi. 10.1002/pmic.202200462

By:

Hecker, Dennis;
Lauber, Michael;
Behjati Ardakani, Fatemeh;
Ashrafiyan, Shamim;
Manz, Quirin;
Kersting, Johannes;
Hoffmann, Markus;
Schulz, Marcel H.;
List, Markus

Publication type:

Article

Gut Microbial Disruption in Critically Ill Patients with COVID-19-Associated Pulmonary Aspergillosis.

Published in:

Journal of Fungi, 2022, v. 8, n. 12, p. 1265, doi. 10.3390/jof8121265

By:

Maurer, H. Carlo;
Schult, David;
Koyumdzhieva, Plamena;
Reitmeier, Sandra;
Middelhoff, Moritz;
Rasch, Sebastian;
List, Markus;
Janssen, Klaus-Peter;
Steiger, Katja;
Protzer, Ulrike;
Schmid, Roland M.;
Neuhaus, Klaus;
Haller, Dirk;
Quante, Michael;
Lahmer, Tobias

Publication type:

Article

On the performance of de novo pathway enrichment.

Published in:

NPJ Systems Biology & Applications, 2017, v. 3, n. 1, p. N.PAG, doi. 10.1038/s41540-017-0007-2

By:

Batra, Richa;
Alcaraz, Nicolas;
Gitzhofer, Kevin;
Pauling, Josch;
Ditzel, Henrik J.;
Hellmuth, Marc;
Baumbach, Jan;
List, Markus

Publication type:

Article

Flimma: a federated and privacy-aware tool for differential gene expression analysis.

Published in:

Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02553-2

By:

Zolotareva, Olga;
Nasirigerdeh, Reza;
Matschinske, Julian;
Torkzadehmahani, Reihaneh;
Bakhtiari, Mohammad;
Frisch, Tobias;
Späth, Julian;
Blumenthal, David B.;
Abbasinejad, Amir;
Tieri, Paolo;
Kaissis, Georgios;
Rückert, Daniel;
Wenke, Nina K.;
List, Markus;
Baumbach, Jan

Publication type:

Article

The limits of molecular signatures for pancreatic ductal adenocarcinoma subtyping.

Published in:

NAR Cancer, 2022, v. 4, n. 4, p. 1, doi. 10.1093/narcan/zcac030

By:

Lautizi, Manuela;
Baumbach, Jan;
Weichert, Wilko;
Steiger, Katja;
List, Markus;
Pfarr, Nicole;
Kacprowski, Tim

Publication type:

Article

Platelet mass cytometry reveals dysregulation of prothrombotic pathways in essential thrombocythemia.

Published in:

Platelets, 2024, v. 35, n. 1, p. 1, doi. 10.1080/09537104.2024.2358244

By:

Dill, Veronika;
Kirmes, Kilian;
Han, Jiaying;
Klug, Melissa;
Rosenbaum, Marc;
Viggiani, Giacomo;
von Scheidt, Moritz;
List, Markus;
Herhaus, Peter;
Ruland, Jürgen;
Bassermann, Florian;
Laugwitz, Karl-Ludwig;
Götze, Katharina S.;
Jost, Philipp J.;
Jilg, Stefanie;
Bloxham, Conor J.;
Raake, Philip W.J.;
Bernlochner, Isabell;
Bongiovanni, Dario

Publication type:

Article

Mass cytometry of platelet-rich plasma: a new approach to analyze platelet surface expression and reactivity.

Published in:

Platelets, 2022, v. 33, n. 6, p. 841, doi. 10.1080/09537104.2021.2009453

By:

Klug, Melissa;
Kirmes, Kilian;
Han, Jiaying;
Lazareva, Olga;
Rosenbaum, Marc;
Viggiani, Giacomo;
von Scheidt, Moritz;
Ruland, Jürgen;
Baumbach, Jan;
Condorelli, Gianluigi;
Laugwitz, Karl-Ludwig;
List, Markus;
Bernlochner, Isabell;
Bongiovanni, Dario

Publication type:

Article

miRNA-26a expression influences the therapy response to carmustine wafer implantation in patients with glioblastoma multiforme.

Published in:

Acta Neurochirurgica, 2019, v. 161, n. 11, p. 2299, doi. 10.1007/s00701-019-04051-8

By:

Sippl, Christoph;
Ketter, Ralf;
Braun, Luisa;
Teping, Fritz;
Schoeneberger, Louisa;
Kim, Yoo Jin;
List, Markus;
Nakhoda, Arjang;
Wemmert, Silke;
Oertel, Joachim;
Urbschat, Steffi

Publication type:

Article

Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survival.

Published in:

Cellular Physiology & Biochemistry (Cell Physiol Biochem Press GmbH & Co. KG), 2019, v. 52, n. 4, p. 787, doi. 10.33594/000000055

By:

Kessler, Sonja M.;
Hosseini, Kevan;
Hussein, Usama Khamis;
Kyoung Min Kim;
List, Markus;
Schultheiß, Christina S.;
Schulz, Marcel H.;
Laggai, Stephan;
Kyu Yun Jang;
Kiemer, Alexandra K.

Publication type:

Article

Emergence of power law distributions in protein-protein interaction networks through study bias.

Published in:

eLife, 2025, p. 1, doi. 10.7554/eLife.99951

By:

Blumenthal, David B.;
Lucchetta, Marta;
Kleist, Linda;
Fekete, Sándor P.;
List, Markus;
Schaefer, Martin H.

Publication type:

Article

KeyPathwayMineR: De Novo Pathway Enrichment in the R Ecosystem.

Published in:

Frontiers in Genetics, 2022, v. 12, p. 1, doi. 10.3389/fgene.2021.812853

By:

Mechteridis, Konstantinos;
Lauber, Michael;
Baumbach, Jan;
List, Markus

Publication type:

Article

MeTEor: an R Shiny app for exploring longitudinal metabolomics data.

Published in:

Bioinformatics Advances, 2024, v. 4, n. 1, p. 1, doi. 10.1093/bioadv/vbae178

By:

Grabert, Gordon;
Dehncke, Daniel;
More, Tushar;
List, Markus;
Kraft, Anke R M;
Cornberg, Markus;
Hiller, Karsten;
Kacprowski, Tim

Publication type:

Article

Inference of differential gene regulatory networks using boosted differential trees.

Published in:

Bioinformatics Advances, 2024, v. 4, n. 1, p. 1, doi. 10.1093/bioadv/vbae034

By:

Galindez, Gihanna;
List, Markus;
Baumbach, Jan;
Völker, Uwe;
Mäder, Ulrike;
Blumenthal, David B;
Kacprowski, Tim

Publication type:

Article

Making mouse transcriptomics deconvolution accessible with immunedeconv.

Published in:

Bioinformatics Advances, 2024, v. 4, n. 1, p. 1, doi. 10.1093/bioadv/vbae032

By:

Merotto, Lorenzo;
Sturm, Gregor;
Dietrich, Alexander;
List, Markus;
Finotello, Francesca

Publication type:

Article

circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging.

Published in:

Bioinformatics Advances, 2023, v. 3, n. 1, p. 1, doi. 10.1093/bioadv/vbad093

By:

Hoffmann, Markus;
Schwartz, Leon;
Ciora, Octavia-Andreea;
Trummer, Nico;
Willruth, Lina-Liv;
Jankowski, Jakub;
Lee, Hye Kyung;
Baumbach, Jan;
Furth, Priscilla A;
Hennighausen, Lothar;
List, Markus

Publication type:

Article

Cracking the black box of deep sequence-based protein–protein interaction prediction.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 2, p. 1, doi. 10.1093/bib/bbae076

By:

Bernett, Judith;
Blumenthal, David B;
List, Markus

Publication type:

Article

Multi-omics regulatory network inference in the presence of missing data.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 5, p. 1, doi. 10.1093/bib/bbad309

By:

Henao, Juan D;
Lauber, Michael;
Azevedo, Manuel;
Grekova, Anastasiia;
Theis, Fabian;
List, Markus;
Ogris, Christoph;
Schubert, Benjamin

Publication type:

Article

systematic comparison of novel and existing differential analysis methods for CyTOF data.

Published in:

Briefings in Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1093/bib/bbab471

By:

Arend, Lis;
Bernett, Judith;
Manz, Quirin;
Klug, Melissa;
Lazareva, Olga;
Baumbach, Jan;
Bongiovanni, Dario;
List, Markus

Publication type:

Article

On the limits of active module identification.

Published in:

Briefings in Bioinformatics, 2021, v. 22, n. 5, p. 1, doi. 10.1093/bib/bbab066

By:

Lazareva, Olga;
Baumbach, Jan;
List, Markus;
Blumenthal, David B

Publication type:

Article

Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-17189-2

By:

Sadegh, Sepideh;
Matschinske, Julian;
Blumenthal, David B.;
Galindez, Gihanna;
Kacprowski, Tim;
List, Markus;
Nasirigerdeh, Reza;
Oubounyt, Mhaned;
Pichlmair, Andreas;
Rose, Tim Daniel;
Salgado-Albarrán, Marisol;
Späth, Julian;
Stukalov, Alexey;
Wenke, Nina K.;
Yuan, Kevin;
Pauling, Josch K.;
Baumbach, Jan

Publication type:

Article

The mRNA-binding Protein TTP/ZFP36 in Hepatocarcinogenesis and Hepatocellular Carcinoma.

Published in:

Cancers, 2019, v. 11, n. 11, p. 1754, doi. 10.3390/cancers11111754

By:

Kröhler, Tarek;
Kessler, Sonja M.;
Hosseini, Kevan;
List, Markus;
Barghash, Ahmad;
Patial, Sonika;
Laggai, Stephan;
Gemperlein, Katja;
Haybaeck, Johannes;
Müller, Rolf;
Helms, Volkhard;
Schulz, Marcel H.;
Hoppstädter, Jessica;
Blackshear, Perry J.;
Kiemer, Alexandra K.

Publication type:

Article

Meta-analysis of proteomics data from osteoblasts, bone, and blood: Insights into druggable targets, active factors, and potential biomarkers for bone biomaterial design.

Published in:

Journal of Tissue Engineering, 2024, p. 1, doi. 10.1177/20417314241295332

By:

Schmidt, Johannes R;
Adamowicz, Klaudia;
Arend, Lis;
Lehmann, Jörg;
List, Markus;
Poh, Patrina SP;
Baumbach, Jan;
Kalkhof, Stefan;
Laske, Tanja

Publication type:

Article

Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside.

Published in:

Clinical Epigenetics, 2021, v. 13, n. 1, p. 1, doi. 10.1186/s13148-021-01047-z

By:

Sarno, Federica;
Benincasa, Giuditta;
List, Markus;
Barabasi, Albert-Lazlo;
Baumbach, Jan;
Ciardiello, Fortunato;
Filetti, Sebastiano;
Glass, Kimberly;
Loscalzo, Joseph;
Marchese, Cinzia;
Maron, Bradley A.;
Paci, Paola;
Parini, Paolo;
Petrillo, Enrico;
Silverman, Edwin K.;
Verrienti, Antonella;
Altucci, Lucia;
Napoli, Claudio;
the International Network Medicine Consortium;
Barabasi, Albert‑Lazlo

Publication type:

Article

Efficient Sample Tracking With OpenLabFramework.

Published in:

Scientific Reports, 2014, p. 1, doi. 10.1038/srep04278

By:

List, Markus;
Schmidt, Steffen;
Trojnar, Jakub;
Thomas, Jochen;
Thomassen, Mads;
Kruse, Torben A.;
Qihua Tan;
Baumbach, Jan;
Mollenhauer, Jan

Publication type:

Article

Drugst.One — a plug-and-play solution for online systems medicine and network-based drug repurposing.

Published in:

Nucleic Acids Research, 2024, v. 52, n. W1, p. W481, doi. 10.1093/nar/gkae388

By:

Maier, Andreas;
Hartung, Michael;
Abovsky, Mark;
Adamowicz, Klaudia;
Bader, Gary D;
Baier, Sylvie;
Blumenthal, David B;
Chen, Jing;
Elkjaer, Maria L;
Garcia-Hernandez, Carlos;
Helmy, Mohamed;
Hoffmann, Markus;
Jurisica, Igor;
Kotlyar, Max;
Lazareva, Olga;
Levi, Hagai;
List, Markus;
Lobentanzer, Sebastian;
Loscalzo, Joseph;
Malod-Dognin, Noel

Publication type:

Article

Cancer driver drug interaction explorer.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W138, doi. 10.1093/nar/gkac384

By:

Hartung, Michael;
Anastasi, Elisa;
Mamdouh, Zeinab M;
Nogales, Cristian;
Schmidt, Harald H H W;
Baumbach, Jan;
Zolotareva, Olga;
List, Markus

Publication type:

Article

DIGGER: exploring the functional role of alternative splicing in protein interactions.

Published in:

Nucleic Acids Research, 2021, v. 49, n. D1, p. D309, doi. 10.1093/nar/gkaa768

By:

Louadi, Zakaria;
Yuan, Kevin;
Gress, Alexander;
Tsoy, Olga;
Kalinina, Olga V;
Baumbach, Jan;
Kacprowski, Tim;
List, Markus

Publication type:

Article

EpiRegio: analysis and retrieval of regulatory elements linked to genes.

Published in:

Nucleic Acids Research, 2020, v. 48, n. W1, p. W193, doi. 10.1093/nar/gkaa382

By:

Baumgarten, Nina;
Hecker, Dennis;
Karunanithi, Sivarajan;
Schmidt, Florian;
List, Markus;
Schulz, Marcel H

Publication type:

Article

Quantitative comparison of within-sample heterogeneity scores for DNA methylation data.

Published in:

Nucleic Acids Research, 2020, v. 48, n. 8, p. e46, doi. 10.1093/nar/gkaa120

By:

Scherer, Michael;
Nebel, Almut;
Franke, Andre;
Walter, Jörn;
Lengauer, Thomas;
Bock, Christoph;
Müller, Fabian;
List, Markus

Publication type:

Article

Alternative splicing impacts microRNA regulation within coding regions.

Published in:

NAR Genomics & Bioinformatics, 2023, v. 5, n. 3, p. 1, doi. 10.1093/nargab/lqad081

By:

Hackl, Lena Maria;
Fenn, Amit;
Louadi, Zakaria;
Baumbach, Jan;
Kacprowski, Tim;
List, Markus;
Tsoy, Olga

Publication type:

Article

Tissue heterogeneity is prevalent in gene expression studies.

Published in:

NAR Genomics & Bioinformatics, 2021, v. 3, n. 3, p. 1, doi. 10.1093/nargab/lqab077

By:

Sturm, Gregor;
List, Markus;
Zhang, Jitao David

Publication type:

Article

spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.

Published in:

Bioinformatics, 2023, v. 39, n. 5, p. 1, doi. 10.1093/bioinformatics/btad276

By:

Boniolo, Fabio;
Hoffmann, Markus;
Roggendorf, Norman;
Tercan, Bahar;
Baumbach, Jan;
Castro, Mauro A A;
Robertson, A Gordon;
Saur, Dieter;
List, Markus

Publication type:

Article

SimBu: bias-aware simulation of bulk RNA-seq data with variable cell-type composition.

Published in:

Bioinformatics, 2022, v. 38, p. ii141, doi. 10.1093/bioinformatics/btac499

By:

Dietrich, Alexander;
Sturm, Gregor;
Merotto, Lorenzo;
Marini, Federico;
Finotello, Francesca;
List, Markus

Publication type:

Article

Robust disease module mining via enumeration of diverse prize-collecting Steiner trees.

Published in:

Bioinformatics, 2022, v. 38, n. 6, p. 1600, doi. 10.1093/bioinformatics/btab876

By:

Bernett, Judith;
Krupke, Dominik;
Sadegh, Sepideh;
Baumbach, Jan;
Fekete, Sándor P;
Kacprowski, Tim;
List, Markus;
Blumenthal, David B

Publication type:

Article

ASimulatoR: splice-aware RNA-Seq data simulation.

Published in:

Bioinformatics, 2021, v. 37, n. 18, p. 3008, doi. 10.1093/bioinformatics/btab142

By:

Manz, Quirin;
Tsoy, Olga;
Fenn, Amit;
Baumbach, Jan;
Völker, Uwe;
List, Markus;
Kacprowski, Tim

Publication type:

Article

BiCoN: network-constrained biclustering of patients and omics data.

Published in:

Bioinformatics, 2021, v. 37, n. 16, p. 2398, doi. 10.1093/bioinformatics/btaa1076

By:

Lazareva, Olga;
Canzar, Stefan;
Yuan, Kevin;
Baumbach, Jan;
Blumenthal, David B;
Tieri, Paolo;
Kacprowski, Tim;
List, Markus

Publication type:

Article

A framework for modeling epistatic interaction.

Published in:

Bioinformatics, 2021, v. 37, n. 12, p. 1708, doi. 10.1093/bioinformatics/btaa990

By:

Blumenthal, David B;
Baumbach, Jan;
Hoffmann, Markus;
Kacprowski, Tim;
List, Markus

Publication type:

Article

EpiGEN: an epistasis simulation pipeline.

Published in:

Bioinformatics, 2020, v. 36, n. 19, p. 4957, doi. 10.1093/bioinformatics/btaa245

By:

Blumenthal, David B;
Viola, Lorenzo;
List, Markus;
Baumbach, Jan;
Tieri, Paolo;
Kacprowski, Tim

Publication type:

Article

Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i436, doi. 10.1093/bioinformatics/btz363

By:

Sturm, Gregor;
Finotello, Francesca;
Petitprez, Florent;
Zhang, Jitao David;
Baumbach, Jan;
Fridman, Wolf H;
List, Markus;
Aneichyk, Tatsiana

Publication type:

Article

Large-scale inference of competing endogenous RNA networks with sparse partial correlation.

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i596, doi. 10.1093/bioinformatics/btz314

By:

List, Markus;
Amirabad, Azim Dehghani;
Kostka, Dennis;
Schulz, Marcel H

Publication type:

Article

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets.

Published in:

Bioinformatics, 2018, v. 34, n. 17, p. i908, doi. 10.1093/bioinformatics/bty553

By:

Schmidt, Florian;
List, Markus;
Cukuroglu, Engin;
Köhler, Sebastian;
Göke, Jonathan;
Schulz, Marcel H

Publication type:

Article

JAMI: fast computation of conditional mutual information for ceRNA network analysis.

Published in:

Bioinformatics, 2018, v. 34, n. 17, p. 3050, doi. 10.1093/bioinformatics/bty221

By:

Hornakova, Andrea;
List, Markus;
Vreeken, Jilles;
Schulz, Marcel H

Publication type:

Article

On the limits of graph neural networks for the early diagnosis of Alzheimer's disease.

Published in:

Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-21491-y

By:

Hernández-Lorenzo, Laura;
Hoffmann, Markus;
Scheibling, Evelyn;
List, Markus;
Matías-Guiu, Jordi A.;
Ayala, Jose L.

Publication type:

Article

Un-biased housekeeping gene panel selection for high-validity gene expression analysis.

Published in:

Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-15989-8

By:

Casas, Ana I.;
Hassan, Ahmed A.;
Manz, Quirin;
Wiwie, Christian;
Kleikers, Pamela;
Egea, Javier;
López, Manuela G.;
List, Markus;
Baumbach, Jan;
Schmidt, Harald H. H. W.

Publication type:

Article