Judith Bernett

2026

• Bernett J., Iversen P., Picciani M., Wilhelm M., Baum K., List M.:
  From Hype to Health Check: Critical Evaluation of Drug Response Prediction Models with DrEval
  (2026)
  DOI: 10.1101/2025.05.26.655288
• Picciani M., Soleymaniniya A., Müller J., Sakhteman A., Tzanakis K., Bernett J., Kahl E., Hamood F., Kersting J., Pourjam M., Nagai LAE., List M., Kuster B., The M., Wilhelm M.:
  Mapping drug mechanisms with ProteomicsDB: unified omics and cell sensitivity data at scale
  In: Nucleic Acids Research 54 (2026), p. D470-D480
  ISSN: 0305-1048
  DOI: 10.1093/nar/gkaf1265

2025

• Kirmes K., Han J., Klug M., Bloxham CJ., Babyak O., Bernett J., Arend L., Manz Q., Raka L., Schwartz L., Hoffmann M., Rosenbaum M., Ruland J., Ciora OA., Louadi Z., Tsoy O., Newaz K., Modica J., Conca Dioguardi C., Peano C., Müller M., Santovito D., Viggiani G., Kühne S., Von Scheidt M., Nicolai L., Wu T., Baumbach J., Chiarito M., Laugwitz KL., Condorelli G., Raake PW., List M., Bernlochner I., Bongiovanni D.:
  Reticulated platelets in coronary artery disease: a multidimensional approach unveils prothrombotic signalling and novel therapeutic targets
  In: European Heart Journal 46 (2025), p. 4901-4917
  ISSN: 0195-668X
  DOI: 10.1093/eurheartj/ehaf694
• Reim T., Hartebrodt A., Blumenthal DB., Bernett J., List M.:
  Deep learning models for unbiased sequence-based PPI prediction plateau at an accuracy of 0.65
  In: Bioinformatics 41 (2025), p. i590-i598
  ISSN: 1367-4803
  DOI: 10.1093/bioinformatics/btaf192
• Stahl M., Straßer LJ., Lio CT., Bernett J., Röttger R., List M.:
  Refinement strategies for Tangram for reliable single-cell to spatial mapping
  In: Bioinformatics (Oxford, England) 41 (2025), p. i552-i560
  ISSN: 1367-4811
  DOI: 10.1093/bioinformatics/btaf194

2024

• Anokian E., Bernett J., Freeman A., List M., Prieto Santamaría L., Tanoli Z., Bonnin S.:
  Machine Learning and Artificial Intelligence in Drug Repurposing—Challenges and Perspectives
  In: Drug Repurposing 1 (2024)
  ISSN: 2941-2528
  DOI: 10.58647/DRUGREPO.24.1.0004
• Bernett J., Blumenthal DB., Grimm DG., Haselbeck F., Joeres R., Kalinina OV., List M.:
  Guiding questions to avoid data leakage in biological machine learning applications
  In: Nature Methods 21 (2024), p. 1444-1453
  ISSN: 1548-7091
  DOI: 10.1038/s41592-024-02362-y
• Bernett J., Blumenthal DB., List M.:
  Cracking the black box of deep sequence-based protein-protein interaction prediction
  In: Briefings in Bioinformatics 25 (2024), Article No.: bbae076
  ISSN: 1467-5463
  DOI: 10.1093/bib/bbae076

2022

• Arend L., Bernett J., Manz Q., Klug M., Lazareva O., Baumbach J., Bongiovanni D., List M.:
  A systematic comparison of novel and existing differential analysis methods for CyTOF data
  In: Briefings in Bioinformatics 23 (2022), Article No.: bbab471
  ISSN: 1467-5463
  DOI: 10.1093/bib/bbab471
• Bernett J., Krupke D., Sadegh S., Baumbach J., Fekete SP., Kacprowski T., List M., Blumenthal DB.:
  Robust disease module mining via enumeration of diverse prize-collecting Steiner trees
  In: Bioinformatics 38 (2022), p. 1600-1606
  ISSN: 1367-4803
  DOI: 10.1093/bioinformatics/btab876
  URL: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btab876/6497106?guestAccessKey=27c2a19b-11b5-4c3c-88d5-f1131e3809a9

2021

• Sadegh S., Skelton J., Anastasi E., Bernett J., Blumenthal DB., Galindez G., Salgado-Albarran M., Lazareva O., Flanagan K., Cockell S., Nogales C., Casas AI., Schmidt HHHW., Baumbach J., Wipat A., Kacprowski T.:
  Network medicine for disease module identification and drug repurposing with the NeDRex platform
  In: Nature Communications 12 (2021), Article No.: 6848
  ISSN: 2041-1723
  DOI: 10.1038/s41467-021-27138-2