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Our publications

Journals

2024

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  1. Galindez G, List M, Baumbach J, Völker U, Mäder U, Blumenthal DB, Kacprowski T (2024) Inference of differential gene regulatory networks from gene expression data using boosted differential trees. Bioinform Adv. 2024 (accepted).

  2. Späth J, Sewald Z, Probul N, Berland M, Almeida M, Pons N, Le Chatellier E, Gines P, Sole C, Juanola A, Pauling J, Baumbach J (2024) Privacy-Preserving Federated Survival Support Vector Machines for Cross-Institutional Time-To-Event Analysis: Implementation and Evaluation. JMIR AI 2024 (in press).

  3. Matchado MS, Rühlemann M, Reimeiter S, Kacprowski T, Frost F, Haller D, Baumbach J, List M (2024) On the limits of 16S rRNA gene-based metagenome prediction and functional profiling. Microb. Genom., 29 February 2024, 10(2), doi: https://doi.org/10.1099/mgen.0.001203 (download from Microbiology Society).

  4. Elkjær ML, Hartebrodt A, Oubounyt M, Weber A, Vitved L, Reynolds R, Thomassen M, Röttger R, Baumbach J, Illes Z (2024) A single-cell multi-omics map of cell-type-specific mechanistic drivers of multiple sclerosis lesions. Neurol Neuroimmunol Neuroinflamm. 2024 (in press)

2023

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  1. Jorgensen MM, Baek R, Bente LM, Lauridsen JT, Hyrlov K, Aboo C, Baumbach J, Kacprowski T, Cotton F, Guttmann CRG, Stensballe A, Illes Z (2023) New enhancing MRI lesions associate with IL-17, neutrophil degranulation and integrin microparticles: multi-omics combined with frequent MRI in multiple sclerosis. Biomedicines 2023, 11(12), 3170; https://doi.org/10.3390/biomedicines11123170 (Download from MDPI).

  2. Spaeth J, Wang RS, Humphrey M, Baumbach J, Loscalzo J (2023) Machine Learning-based Integration of Network Features and Chemical Structure of Compounds for SARS-CoV-2 Drug Effect Analysis. CPT Pharmacometrics Syst Pharmacol.  2023 Nov 10. doi: 10.1002/psp4.13076. (Download from ASCPT).

  3. Taheri A, RahimiZadeh K, Beheshti A, Baumbach J, Rao RV, Mirjalili S, Gandomi AH (2023) Partial reinforcement optimizer: An evolutionary optimization algorithm. Expert Systems with Applications. 122070, 19 October 2023 https://doi.org/10.1016/j.eswa.2023.122070 (Download from ScienceDirect). 

  4. Oubounyt M, Adlung L, Patroni F, Wenke NK, Maier A, Hartung M, Baumbach J, Elkjaer ML (2023) Inference of differential key regulatory networks and mechanistic drug repurposing candidates from scRNAseq data with SCANet. Bioinformatics 2023 Nov 1;39(11):btad644, doi: 10.1093/bioinformatics/btad64 (download from Oxford Academic).

  5. Adamowicz K, Arend L, Maier A, Schmidt JR, Kuster B, Tsoy O, Zolotareva O, Baumbach J, Laske T (2023) Proteomic Meta-Study Harmonization, Mechanotyping and Drug Repurposing Candidate Prediction with ProHarMeD. NPJ Syst Biol Appl. 2023 Oct 10;9(1):49, doi: 10.1038/s41540-023-00311-7 (download from Nature).

  6. Hackl LM, Fenn A, Louadi Z, Baumbach J, Kacprowski T, List M, Tsoy O (2023) Alternative splicing impacts microRNA regulation within coding regions. NAR Genom Bioinform. 2023 Sep 11;5(3):lqad081, doi: 10.1093/nargab/lqad081 (download from NAR)

  7. Hoffmann M, Schwartz L, Ciora OA, Trummer N, Willruth LL, Jankowski J, Lee HK, Baumbach J, Furth P, Hennighausen L, List M (2023) circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. Bioinform Adv. 2023 Jul 8;3(1):vbad093 (download from Oxford Academic).

  8. Rogg M, Maier JI, Helmstädter M, Sammarco A, Kliewe F, Kretz O, Weißer L, van Wymersch C, Findeisen K, Koessinger AL, Tsoy O, Baumbach J, Grabbert M, Werner M, Huber TB, Endlich N, Schilling O, Schell C (2023) A YAP/TAZ – ARHGAP29 – RhoA signaling axis regulates podocyte protrusions and integrin adhesions. Cells 2023 Jul 6;12(13):1795 (download from MDPI).

  9. Carlin DE,Larsen SJ, Sirupurapu V, Cho MH, Silverman EK, Baumbach J, Ideker T (2023) Hierarchical association of COPD to principal genetic components of biological systems. PLoS One. 2023 May 25;18(5):e0286064. (download from PLoS)

  10. Sarkar S, Lucchetta M, Maier A, Abdrabbou MM, Baumbach J, List M, Schaefer MH, Blumenthal DB (2023) Online bias-aware disease module mining with ROBUST-Web. Bioinformatics 2023 May 26;35(6):btad345 (download from Oxford Academic).

  11. Lobentanzer S, Aloy P, Baumbach J, Bohar B, Charoentong P, Danhauser K, Doğan T, Dreo J, Dunham I, Fernandez-Torras A, Gyori BM, Hartung M, Hoyt CT, Klein C, Korcsmaros T, Maier A, Mann M, Ochoa D, Pareja-Lorente E, Popp F, Preusse M, Probul N, Schwikowski B, Sen B, Strauss MT, Turei D, Ulusoy E, Waltemath D, Wodke JAH, Saez-Rodriguez J (2023) Democratising Knowledge Representation with BioCypher. Nat. Biotechnol. 2023 Jun 19; doi: 10.1038/s41587-023-01848-y (download from Naturę).

  12. Kahlon PS, Förner A, Muser M, Oubounyt M, Gigl M, Hammerl R, Baumbach J, Hückelhoven R, Dawid C, Stam R (2023) Laminarin-triggered defence responses are geographically dependent in natural populations of Solanum chilense. J. Exp. Bot. 2023 May 19;74: 3240–3254 (download from Oxford Academic).

  13. Del Moral-Morales A, Salgado-Albarrán M, Sánchez-Pérez Y, Wenke NK, Baumbach J, Soto-Reyes E (2023) CTCF And Its Multi-partner Network For Chromatin Regulation. Cells 2023 May 10;12(10),1357. (download from MDPI)

  14. Fenn A, Tsoy O, Faro T, Rössler F, Dietrich A, Kersting J, Louadi Z, Lio CT, Völker U, Baumbach J, Kacprowski T, List M (2023) Alternative splicing analysis benchmark with DICAST. NAR Genom Bioinform. 2023 May 30;5(2):Iqad044 (download from Oxford Academic).

  15. Boniolo F, Hoffmann M, Roggendorf N, Tercan B, Baumbach J, Castro MAA, Robertson AG, Saur D, List M (2023) spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape. Bioinformatics 2023 Apr 21;btad276. (download from Bioinformatics)

  16. Pai S, Hui S, Weber P, Narayan S, Whitley O, Li P, Labrie V, Baumbach J, Wheeler A, Bader G (2023) Multi-scale systems genomics analysis predicts pathways, cell types and drug targets involved in normative human cognition variation. Cereb Cortex 2023 Apr 27;bhad142. (download from Cerebral Cortex)

  17. Hoffmann M, Trummer N, Schwartz L, Jankowski J, Lee HK, Willruth LL, Lazareva O, Yuan K, Baumgarten N, Schmidt F, Baumbach J, Schulz MH, Blumenthal DB, Hennighausen L, List M (2023) TF-Prioritizer: a java pipeline to prioritize condition-specific transcription factors. GigaScience 2022 Dec 28;12:giad026. (download from GigaScience)

  18. Matschinske J, Späth J, Bakhtiari M, Probul N, Majdabadi MMK, Nasirigerdeh R, Torkzadehmahani R, Hartebrodt A, Orbán B, Fejér S, Zolotareva O, Das S, Baumbach L, Pauling JK, Tomašević O, Bihari B, Bloice M, Donner N, Fdhila W, Frisch T, Hauschild AC, Heider D, Holzinger A, Hötzendorfer W, Hospes J, Kacprowski T, Kastelitz M, List M, Mayer R, Moga M, Müller H, Pustozerova A, Röttger R, Saak CC, Saranti A, Schmidt HHHW, Tschohl C, Wenke NK, Baumbach J (2023) The FeatureCloud Platform for Federated Learning in Biomedicine: A Unified Approach. J Med Internet Res. 2023 Jul 12;25:e42621(download from JMIR).

  19. Brauneck A, Schmalhorst L, Majdabadi MMK, Bakhtiari M, Völker U, Baumbach J, Baumbach L, Buchholtz G (2023) Federated Machine Learning, Privacy-Enhancing Technologies, and Data Protection Laws in Medical Research: A scoping Review. J Med Internet Res. 2023 Mar 30;25:e41588. (download from JMIR)

  20. Oubounyt M, Elkjaer ML, Laske T, Grønning AGB, Moeller MJ, Baumbach J (2023) De-novo reconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters. NAR Genome Bioinform. 2023 Mar 3;5(1):lqad018. (download from NAR)

  21. Lio CT, Grabert G, Louadi Z, Fenn A, Baumbach J, Kacprowski T, List M, Tsoy O (2023) Systematic analysis of alternative splicing in time course data using Spycone. Bioinformatics 2023 Jan 1;39(1):btac846. (download from Bioinformatics)

  22. Brauneck A, Schmalhorst L, Majdabadi MMK, Bakhtiari M, Völker U, Saak CC, Baumbach J, Baumbach L, Buchholtz G (2023) Federated Machine Learning in Light of Data Protection Compliant Research. Nature Mach. Intell. 2023 Jan 25;5:2-4. (download from Nature)

2022

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  1. Sadegh S, Skelton J, Anastasi E, Maier A, Adamowicz K, Möller A, Kriege NM, Kronberg J, Haller T, Kacprowski T, Wipat A, Baumbach J, Blumenthal DB (2022) Lacking mechanistic disease definitions and corresponding association data hamper progress in network medicine and beyond. Nat. Commun. 2023 Mar 25;14(1):1662. (download from Nature)

  2. Galindez GG, Sadegh S, Baumbach J, Kacprowski T, List M (2022) Network-based approaches for modeling disease regulation and progression. Comput. Struct. Biotechnol. J. 2022 Dec 16;21:780-795. (download from Elsevier)

  3. Elkjaer ML, Simon L, Frisch T, Bente LM, Kacprowski T, Thomassen M, Reynolds R, Baumbach J, Röttger R, Illes Z (2022) Hypothesis of a potential BrainBiota and its relation to CNS autoimmune inflammation. Front. immunol. 2022 Dec 2;13:1043579. (download from Frontiers) 

  4. Lautizi M, Baumbach J, Weichert W, Steiger K, List M, Pfarr N, Kacprowski T (2022) The Limits of Molecular Signatures for Pancreatic Ductal Adenocarcinoma Subtyping. NAR Cancer 2022 Oct 17;4(4):zcac030. (download from NAR Cancer)

  5. Cao H, Zhang Y, Baumbach J, Burton PR, Dwyer D, Koutsouleris N, Matschinske J, Marcon Y, Rajan S, Rieg T, Ryser-Welch P, Späth J, The COMMITMENT consortium, Herrmann C, Schwarz E (2022) dsMTL - a computational framework for privacy-preserving, distributed multi-task machine learning. Bioinformatics 2022 Sep 8;btac616. (download from Oxford Academic)

  6. Späth J, Matschinske J, Kamanu FK, Murphy SA, Zolotareva O, Bakhtiari M, Antman EM, Loscalzo J, Brauneck A, Schmalhorst L, Buchholtz G, Baumbach J (2022) Privacy-aware multi-institutional time-to-event studies. PLoS Digit Health. 2022 Sep 6;1(9): e0000101. (download from PLoS)

  7. Casas AI, Hassan AA, Manz Q, Wiwie C, Kleikers P, Egea J, López MG, List M, Baumbach J, Schmidt HHHW (2022) Un-biased housekeeping gene panel selection for high-validity gene expression analysis. Sci Rep. 2022 Jul 19;12(1):12324. (download from Nature)

  8. Hutzfeldt A, Tan Y, Bonin L, Beck B, Baumbach J, Lassé M, Demir F, Rinschen M (2022) Consensus draft of the native mouse podocyte-ome. Am. J. Physiol. Renal Physiol. 2022 Aug 1;323(2):F182-F197. (download from Am. J. Physiol. Renal Physiol.)

  9. Adamowicz K, Maier A, Baumbach J, Blumenthal DB (2022) Online in silico validation of disease and gene sets, clusterings, or subnetworks with DIGEST. Brief Bioinform. 2022 Jul 18;23(4):bbac247. (download from Oxford Academic)

  10. Dietrich A, Matchado MS, Zwiebel M, Ölke B, Lauber M, Lagkouvardos I, Baumbach J, Haller D, Brandl B, Skurk T, Hauner H, Reitmeier S, List M (2022) Namco: A microbiome explorer. Microb. Genom. 2022 Aug 2;8(8). (download from Microbiology Society)

  11. Hartung M, Anastasi E, Mamdouh Z, Nogales CC, Schmidt HHH, Baumbach J, Zolotareva O, List M (2022) Cancer Driver Drug Interaction Explorer. Nucleic Acids Res. 2022 May 17;gkac384. (download from Oxford Academic)

  12. Boxberg M, Stoegbauer F, Lautizi M, Kriegsmann M, Winter H, Muley T, Kriegsmann K, Jesinghaus M, Baumbach J, Schüffler P, Weichert W, Kacprowski T (2022) Tumour Cell Budding and Spread Through Air Spaces in Squamous Cell Carcinoma of the Lung – Determination and Validation of optimal prognostic cut-offs. Lung Cancer 2022 May 2;169:1-12. (download from Elsevier)

  13. Rose TD, Bechtler T, Ciora OA, Le KAL, Molnar F, Koehler N, Baumbach J, Röttger R, Pauling JK (2022) MoSBi: Automated signature mining for molecular stratification and subtyping. Proc Natl Acad Sci U.S.A. 2022 Apr 11; 119 (16) e2118210119. (download from PNAS)

  14. Elkjær ML, Röttger R, Baumbach J, Illes Z (2022) A systematic review of tissue and single cell transcriptome/proteome studies of the brain in multiple sclerosis. Front. immunol. 2022 Mar 2;13:761225. (download from Frontiers)

  15. Hauschild AC, Lemanczyk M, Matschinske J, Frisch T, Zolotareva O, Holzinger A, Baumbach J, Heider D (2022) Federated Random Forests can improve local performance of predictive models for various health care applications. Bioinformatics 2022 Feb 9;btac065. (download from Oxford Academic)

  16. Salgado-Albarrán M, Späth J, González-Barrios R, Soto-Reyes E*, Baumbach J* (2022) CTCFL (BORIS) regulates the PI3K-Akt signaling pathway in ovarian cancer - A new mechanistic target for personalized therapy and biomarker development. NPJ Syst Biol Appl. 2022 Feb 7;8(1):5. [* joint last author] (download from Nature)

  17. Mechteridis K, Lauber M, Baumbach J, List M (2022) KeyPathwayMineR: de novo pathway enrichment in the R ecosystem. Front. Genet. 2022 Jan 31;12:812853. (download from Frontiers)

  18. Nasirigerdeh R, Torkzadehmahani R, Matschinske J, Frisch T, List M, Späth J, Weiss S, Völker U, Pitkänen E, Heider D, Wenke DK, Kaissis G, Rueckert D, Kacprowski T, Baumbach J (2021) sPLINK: A Hybrid Federated Tool as a Robust Alternative to Meta-Analysis in Genome-Wide Association Studies. Genome Biol. 23(32), Jan 24, 2022. (download from Genome Biology)

  19. Torkzadehmahani R, Nasirigerdeh R, Blumenthal DB, Kacprowski T, List M, Matschinske J, Spaeth J, Wenke NK, Baumbach J (2021) Privacy-preserving Artificial Intelligence Techniques in Biomedicine. Methods Inf Med. 2022 Jan 21. doi: 10.1055/s-0041- 1740630. (download from Thieme)

  20. Poh PSP, Lingner T, Kalkhof S, Märdian S, Baumbach J, Dondl P, Duda GN, Checa S (2022) Enabling technologies towards personalization of scaffolds for large bone defect regeneration. Curr Opin Biotechnol. 2022 Jan 7;74:263-270. (download from Elsevier)

  21. Bernett J, Krupke D, Sadegh S, Baumbach J, Fekete SP, Kacprowski T, List M, Blumenthal DB (2022) Robust disease module mining via enumeration of diverse prize- collecting Steiner trees. Bioinformatics 2022 Jan 4;btab876. (download from Oxford Academic)

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2021

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  1. Arend L, Bernett J, Manz Q, Klug M, Lazareva O, Baumbach J, Bongiovanni D, List M (2021) A systematic comparison of novel and existing differential analysis methods for CyTOF data. Brief Bioinform 2021 Nov 30;bbab471. (download from Oxford Academic)

  2. Zolotareva O, Nasirigerdeh R, Matschinske J, Torkzadehmahani R, Bakhtiari M, Frisch T, Späth J, Blumenthal DB, Abbasinejad A, Tieri P, Kaissis G, Rueckert D, Wenke NK, List M, Baumbach J (2021) Flimma: A federated and privacy-aware tool for differential gene expression analysis. Genome Biol. 2021 Dec 14;22(1):338. (download from Genome Biology)

  3. Klug M, Kirmes K, Han J, Lazareva O, Rosenbaumd M, Viggiani G, von Scheidt M, Ruland J, Baumbach J, Condorelli G, Laugwitz KL, List M, Bernlochner I, Bongiovannia D (2021)Mass cytometry of platelet-rich plasma: a new approach to analyze platelet surface expression and reactivity. Platelets 2021 Dec 27;1-8. (download from Taylor & Francis Online)

  4. Louadi Z, Elkjaer ML, Klug M, Lio CT, Fenn A, Illes Z, Bongiovanni D, Baumbach J, Kacprowski T, List M,Tsoy O (2021) Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. Genome Biol. 22(327), Dec 2 2021. (download from Genome Biology)

  5. Sadegh S, Skelton J, Anastasi E, Bernett J, Blumenthal DB, Galindez G, Salgado-Albarrán M, Lazareva O, Flanagan K, Cockell S, Nogales C, Casas AI, Schmidt HHHW, Wipat A, Baumbach J, Kacprowski T (2021) Network medicine for disease module identification and drug repurposing - The NeDRex platform. Nat Commun. 2021 Nov 25;12(1):6848. (download from Nature Commun.)

  6. Klug M, Lazareva O, Kirmes K, Rosenbaum M, Lukas M, Weidlich S, Spinner CD, von Scheidt M, Gosetti R, Baumbach J, Ruland J, Condorelli G, Laugwitz KL, List M, Bernlochner I, Bongiovanni D (2021) Platelet Surface Protein Expression and Reactivity upon TRAP Stimulation after BNT162b2 Vaccination. Thromb Haemost 2021 Aug 13. doi: 10.1055/s-0041-1733934. (download from Thieme)

  7. Casas AI, Hassan A, Baumbach J, Kleinschnitz H, Schmidt H (2021) Network pharmacology-based therapy for ischemic stroke: A new concept of medicine. Eur. J. Clin. 51(122-122), June 1, 2021. (download from PNAS)

  8. Matschinske J, Alcaraz N, Benis A, Golebiewski M, Grimm DG, Heumos L, Kacprowski T,  Lazareva O, List M, Louadi Z, Pauling JK, Pfeifer N, Röttger R, Schwämmle V, Sturm G, Traverso A, van Steen K, Vaz de Freitas M, Silva GCV, Wee L, Wenke NK, Zanin M, Zolotareva O, Baumbach J, Blumenthal DB (2021) The AIMe registry for artificial intelligence in biomedical research. Nat Methods  18:1128-1131, Aug 25 2021. (download from Nature)

  9. Mohammadnejad A, Baumbach J, Li W, Lund J, Larsen MJ, Li S, Mengel-From J, Michel TM, Christiansen L, Christensen K, Hjelmborg J, Tan Q (2021) Differential lncRNA expression profiling of cognitive function in middle and old aged monozygotic twins using generalized association analysis. J. Psychiatr. Res. 140(p197-204), August 2021.(download from Science Direct)

  10. Parise MTD, Parise D, Aburjaile FF, ACP Gomide, Kato RB, Raden M, Backofen R, Azevedo VA, Baumbach J (2021) An integrated database of small RNAs and their interplay with transcriptional gene regulatory networks in corynebacteria. Front Microbiol. (download from Frontiers)

  11. Wolff JR, Pauling JK, Keck AJ, Baumbach J (2021) Success Factors of Artificial Intelligence Implementation in Healthcare. Front. Digit. Health, 16 June 2021. (download from frontiers)

  12. Matchado MS, Lauber M, Reitmeier S, Kacprowski T, Baumbach J, Haller D, List M (2021) Network analysis methods for studying microbial communities: A mini review. Comput Struct Biotechnol J. 2021 May. (download from NCBI)

  13. Mohammadnejad A, Li W, Lund JB, Li S, Larsen MJ, Mengel-From J, Michel TM, Christiansen L, Christensen K, Baumbach J, Hjelmborg J, Tan Q (2021)  Global gene expression profiling and transcription factor network analysis of cognitive aging in monozygotic twins. (download from Front Genet) 

  14. Lange-Kuettner C, Averbeck BB, Hentschel M, Baumbach J (2021) Intelligence Matters for Stochastic Feedback Processing during Sequence Learning in Adolescents and Young Adults. Intelligence 2021 86 (May): 101542 (download from ScienceDirect)

  15. Blumenthal DB, Boria N, Bougleux S, Brun L, Gamper J, Gaüzère B (2021) Scalable generalized median graph estimation and its manifold use in bioinformatics, clustering, classification, and indexing. Inf Syst. 2021 (download from ScienceDirect)

  16. Blumenthal DB, Gamper J, Bougleux S, Brun L (2021) Upper bounding the graph edit distance based on rings and machine learning. Int J Pattern Recognit Artif Intell. 2021 (download from World Scientific) 

  17. Sarno F, Benincasa G, List M, Barabasi AL, Baumbach J, Ciardiello F, Filetti S, Glass K, Loscalzo J, Marchese C, Maron BA, Paci P, Parini P, Petrillo E, Silverman EK, Verrienti A, Altucci L, Napoli C (2021) Clinical Epigenetics Settings for Cancer and Cardiovascular Diseases: Real-life Applications of Network Medicine at the Bedside. Clinical Epigenetics 2021 Mar 30;13(1):66 (download from BMC)

  18. Manz Q, Tsoy O, Fenn A, Baumbach J, Völker U, List M, Kacprowski T (2021) ASimulatoR: splice-aware RNA-Seq data simulation. Bioinformatics 2021 Feb 27;btab142.

  19. Parise D, Parise MTD, Kataka E, Kato RB, List M, Tauch A, Azevedo VAC, Baumbach J. (2021) On the Consistency between Gene Expression and the Gene Regulatory Network of Corynebacterium glutamicum. Netw Syst Med. 2021 Mar 8;4(1):51-59. (download from liebertpub)

  20. Salgado M, Navarro-Delgado EI, Del Moral-Morales A, Alcaraz N, Baumbach J, González- Barrios R, Soto-Reyes E (2021) Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection. NPJ Syst Biol Appl. 2021 May 24;7(1):21. (download from Nature)

  21. Parise D, Parisa MTD, Gomida ACP, Aburjaile FF, Kato RB, Salgado M, Tauch A, Azevedo V, Baumbach J (2021)  The transcriptional regulatory network of Corynebacterium pseudotuberculosis. Microorganisms 2021, 9(2), 415 (download from MDPI)

  22. Scherer M, Schmidt F, Lazareva O, Walter J, Baumbach J, Schulz MH, List M (2021) Machine learning for deciphering cell heterogeneity and gene regulation. Nat Comp Sci. 1, pages183–191(2021) (download from Nature)

  23. Lazareva O, Baumbach J, List M, Blumenthal DB (2021) On the limits of active module identification. Brief Bioinform. 2021 Mar 29;bbab066 (download from Oxford Academic)

  24. Abellan-Schneyder I, Matchado MS, Reitmeier S, Sommer A, Sewald Z, Baumbach J, List M, Neuhaus K (2021) Primer, pipelines, parameters – issues in 16S rRNA gene sequencing. mSphere 2021 Feb 24;6(1):e01202-20 (download from mSphere)

  25. Elkjaer ML, Nawrocki A, Kacprowski T, Lassen P, Simonsen AH, Marignier R, Sejbaek T, Nielsen HH, Wermuth L, Rashid AY, Høgh P, Sellebjerg F, Reynolds R, Baumbach J, Larssen MR, Illes Z (2021) CSF proteome in multiple sclerosis subtypes related to brain lesion transcriptomes. Sci Rep. 2021 Feb 18;11(1):4132 (download from Nature)

  26. Lazareva O, Canzar S, Yuan K, Baumbach J, Blumenthal D, Tieri P, Kacprowski T, List M (2021) BiCoN: Network-constrained biclustering of patients and omics data. Bioinformatics (download from Oxford Academic)

  27. Elkjaer M, Frisch T, Tonazzolli A, Röttger R, Reynolds R, Baumbach J, Illes Z (2021) Unbiased examination of genome-wide human endogenous retrovirus (HERV) transcripts in MS brain lesions. Mult Scler 2021 19:1352458520987269 (download from sage journal)

  28. Gronning AGB, Oubounyt M, Kanev K, Lund J, Kacprowski T, Zehn D, Röttger R, Baumbach J (2021) Enabling single-cell trajectory network enrichment. Nat Comp Sci. 1, p153–163(2021) (download from Nature)

  29. Mohammadnejad A, Sorensen M, Baumbach J, Mengel-From J, Li W, Lund J, Shuxia Li, Christiansen L, Christensen K, Hjelmborg J, Tan Q (2021) Novel DNA methylation marker discovery by assumption-free genome-wide association analysis of cognitive function in twins. Aging Cell 2021 Feb 2:e13293. (download from Wiley Online Library)

  30. Galindez G, Matschinske J, Rose TD, Sadegh S, Salgado-Albarrán M, Späth J, Baumbach J, Pauling JK (2021) Computational methods for drug repurposing: Lessons from the COVID-19 pandemic. Nat Comp Sci. 1, 33–41(2021) (download from Nature)

  31. Bongiovanni D, Klug M, Lazareva O, Weidlich S, Biasi M, Ursu S, Warth S, Buske C, Lukas M, Spinner C, von Scheidt M, Condorelli B, Baumbach J, Laugwitz KL, List M, Bernlochner I (2021) SARS-CoV-2 infection is associated with a pro-thrombotic platelet phenotype. Cell Death Dis.  2021 Jan 5;12(1):50. (download from Nature)

  32. Hoffmann M, Pachl E, Hartung M, Stiegler V, Baumbach J, Schulz M, List M (2021) SPONGEdb: A pan-cancer resource for competing endogenous RNA interactions. NAR Cancer, Volume 3, Issue 1, March 2021, zcaa042 (download from Oxford Academic)

2020

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  1. 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 RD, Fritz A, Fuchs S, Hattab G, Hauschild AC, Heider D, Hoffmann M, Hölzer M, Hoops S, Kaderali L, Kalvari I, von Kleist M, Kmiecinski R, Kühnert D, Lasso G, Libin P, List M, Löchel HF, Martin MJ, Martin R, Matschinske J, McHardy AC, Mendes P, Mistry J, Navratil V, Nawrocki EP, O'Toole ÁN, Ontiveros-Palacios N, Petrov AI, Rangel-Pineros G, Redaschi N, Reimering S, Reinert K, Reyes A, Richardson L, Robertson DL, Sadegh S, Singer JB, Theys K, Upton C, Welzel M, Williams L, Marz M (2020) Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Brief Bioinform. 2020 Nov 4:bbaa232. (download from Oxford Academic)

  2. Blumenthal DB, Baumbach J, Hoffmann M, Kacprowski T, List M (2020) A framework for modeling epistatic interaction. Bioinformatics btaa990 (download from Oxford Academic)

  3. Lund JB, Li W, Mohammadnejad A, Li S, Baumbach J, Tan Q (2020) EWASex – An efficient R-package to predict sex in epigenome-wide association studies. Bioinformatics 2020 Dec 11:btaa949. (download from Oxford Academic)

  4. Vasconcelos MH, Alcaro S, Arechavala-Gomeza V, Baumbach J, Borges F, Brevini TAL, De Las Rivas J, Devaux Y, Hozak P, Keinänen-Toivola MM, Lattanzi G, Mohr T, Murovska M, Prusty BK, Quinlan RA, Pérez-Sala D, Scheibenbogen C, Schmidt HHHW, Silveira I, Tieri P, Tolios A, Riganti C (2020) Joining European Scientific Forces to Face Pandemics. Trends Microbiol. (download from Cell)

  5. Frost F, Kacprowski T, Rühlemann M, Pietzner M, Bang C, Franke A, Nauck M, Völker U, Völzke H, Dörr M, Baumbach J, Sendler M, Schulz C, Mayerle J, Weiss FU, Homuth G, Lerch MM (2020) Long-term instability of the intestinal microbiome is associated with metabolic liver disease, low microbiota diversity, diabetes mellitus and impaired exocrine pancreatic function. Gut 2020 Nov 9;gutjnl-2020-322753. (download from BMJ​ Gut​)

  6. Zanin M, Aitya N, Basilio J, Baumbach J, Benis A, Behera C, Bucholc M,Castiglione F, Chouvarda I, Comte B, Dao T-T, Ding X, Pujos-Guillot E, Filipovic N, Finn D, Glass D, Harel N, Iesmantas T, Ivanoska I, Joshi A, Zouaoui Boudjeltia K, Kaoui B, Kaur D, Maguire L,McClean P, McCombe N, Miranda JL, Moisescu M, Pappalardo F, Polster A, Prasad G, Rozman D, Sacala I, Sanchez-Bornot J, Schmid J, Sharp T, Solé J, Spiwok V, Spyrou G, Stalidzans E, Stres B, Sustersic T, Symeonidis I, Tieri P, Todd S, Van Steen K, Veneva M, Wang D-H, Wang H, Wang H, Watterson S, Wong-Lin KF, Yang S, Zou X, Schmidt H. (2020) An Early Stage Researcher’s Primer on Systems Medicine Terminology. Netw Syst Med. 2021 Feb 25;4(1):2-50. (download from liebertpub) 

  7. do Canto LM, Barros-Filho MC, Rainho CA, Marinho D, Kupper BEC, Begnami MDFS, Scapulatempo-Neto C, Havelund BM, Lindebjerg J, Marchi FA, Baumbach J, Aguiar S Jr, Rogatto SR (2020) Comprehensive analysis of DNA methylation and prediction of response to neoadjuvant therapy in locally advanced rectal cancer. Cancers 2020 Oct 22;12(11):E3079 (download from MDPI)

  8. Pai S, Weber P, Isserlin R, Kaka H, Hui S, Shah MA, Giudice L, Giugno R, Nohr AK, Baumbach J, Bader GD (2020) netDx: Software for building interpretable patient classifiers by multi-omic data integration using patient similarity networks. F1000 Research 15 OCT 2020, 9:1239. (download from F1000Reserach)

  9. Matschinske J, Salgado-Albarrán M, Sadegh S, Bongiovanni D, Baumbach J, Blumenthal DB (2020) Individuating possibly repurposable drugs and drug targets for COVID-19 treatment via hypothesis-driven systems medicine using CoVex. Assay Drug Dev Technol. 2020 Nov 6. (download from liebertpub)

  10. Weber P, Pauling JK, List M, Baumbach J (2020) BALSAM - An Interactive Online Platform for Breath Analysis, Visualization and Classification. Metabolites 2020 Oct 2;10(10):E393. (download from MDPI)

  11. Mohammadnejad A, Nygaard M, Li S, Zhang D, Xu C, Li W, Lund J, Christiansen L, Baumbach J, Christensen K, Hjelmborg J, Tan Q (2020) Generalized correlation coefficient for genome-wide association analysis of cognitive ability in twins. Aging 2020 Nov 24;12(22):22457-22494. (download from Aging)

  12. Faldoni FLC, Villacis RAR, Canto LM, Fonseca-Alves CE, Cury SS, Larsen SJ, Aagaard MM, Souza CP, Scapulatempo-Neto C, Osório CABT, Baumbach J, Marchi FA, Rogatto SR (2020) Inflammatory breast cancer: clinical implications of genomic alterations and mutational profiling. Cancers 2020 Sep 30;12(10): E2816. (download from MDPI)

  13. Elbatreek MH, Sadegh S, Anastasi E, Guney E, Nogales C, Kacprowski T, Hassan AA, Teubner A, Huang PH, Hsu CY , Schiffers PM, Janssen GM, Kleikers PWM, Wipat A, Baumbach J, De Mey JGR, Schmidt HHHW (2020) NOX5-induced uncoupling of endothelial NO synthase is a causal mechanism and theragnostic target of an age-related hypertension endotype. PLoS Biology 18 (11): e3000885. (download from PLoS Biology)

  14. Bouter Y, Kacprowski T, Rößler F, Jensen LR, Kuss AW, Bayer TA. (2020) miRNA Alterations Elicit Pathways Involved in Memory Decline and Synaptic Function in the Hippocampus of Aged Tg4-42 Mice. Front Neurosci. 2020 Sep 10;14:580524. (download from Frontiers)

  15. Louadi Z, Yuan K, Gress A, Tsoy O, Kalinina O, Baumbach J, Kacprowski T, List M (2020) DIGGER: Exploring the functional role of alternative splicing in protein interactions. Nucleic Acids Res. 2020 Sep 25:gkaa768. (download from Oxford Academic)

  16. Frisch T, Elkjaer ML, Reynolds R, Michel TM, Kacprowski T, Burton M, Kruse TA, Thomassen M, Baumbach J, Illes Z. (2020) Multiple Sclerosis Atlas: A Molecular Map of Brain Lesion Stages in Progressive Multiple Sclerosis. Netw Syst Med. 2020 Aug 27;3(1):122-129. (download from liebertpub)

  17. Comte B, Baumbach J, Benis A, Basílio J, Debeljak N, Flobak Å, Franken C, Harel N, He F, Kuiper M, Méndez Pérez JA, Pujos-Guillot E, Režen T, Rozman D, Schmid JA, Scerri J, Tieri P, Van Steen K, Vasudevan S, Watterson S, Schmidt HHHW. (2020) Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine. Netw Syst Med. 2020 Jul 6;3(1):67-90. (download from liebertpub)

  18. Parini P, Altucci L, Balligand JL, Baumbach J, Ferdinandy P, Filetti S, Maron BA, Petrillo E, Silverman EK, Barabasi AL, Loscalzo J (2020) The Network Medicine Imperative and the Need for an International Network Medicine Consortium. Am J Med. 2020;133(9):e451-e454. (download from amjmed)

  19. Helmer S, Blumenthal DB, Paschen K. (2020) What is meaningful research and how should we measure it? Scientometrics 125, pages153–169 (2020). (download from Springer) 

  20. de Witt J, Oetermann S, Parise M, Parise D, Baumbach J, Steinbüchel A. Identification of a global regulator and its involvement in the regulation network of rubber degradation in Gordonia polyisoprenivorans VH2. Appl Environ Microbiol.  2020 Jul 20;86(15):e00774-20. (download from aem.asm)

  21. Maron BA, Altucci L, Balligand JL, Baumbach J, Ferdinandy P, Filetti S, Parini P, Petrillo E, Silverman EK, Barabási AL, Loscalzo J; International Network Medicine Consortium. (2020) A Global Network for Network Medicine. NPJ Syst Biol Appl. 2020 Aug 31;6(1):29 (download from Nature)

  22. Flosbach M, Oberle SG, Scherer S, Zecha J, von Hoesslin M, Wiede F, Chennupati V, Cullen JG, List M, Pauling J, Baumbach J, Kuster B, Tiganis T, Zehn D (2020) PTPN2 deficiency enhances programmed T cell expansion and survival capacity of activated T cells. Cell Rep. 2020 Jul 28;32(4):107957. (download from Cell Reports)

  23. Sadegh S, Matschinske J, Blumenthal DB, Galindez G, Kacprowski T, List M, Nasirigerdeh R, Oubounyt M, Pichlmair A, Rose TD, Salgado-Albarrán M,
    Späth J, Stukalov A, Wenke NK, Yuan K, Pauling JK, Baumbach J (2020) Exploring the SARS-CoV-2 virus-host-drug interactome for drug repurposing. Nat Commun. 2020 Jul 14;11(1):3518. (download from Nature)

  24. Gronning A, T Doktor, Larsen S, Petersen U, Holm L, Bruun G, Hansen M, Hartung A, Baumbach J, Andresen B (2020) DeepCLIP: Predicting the effect of mutations on protein-RNA binding with Deep Learning. Nucleic Acids Res. 2020 Jul 27;48(13):7099-7118. (download from Oxford Academic)

  25. Reitmeier S, Kiessling S, Clavel T, List M, Almeida EL, Ghosh TS, Neuhaus K, Grallert H, Linseisen J, Skurk T, Brandl B, Breuninger T, Troll M, Rathmann W, Linkohr W, Hauner H, Lauders M, Franke A, Le Roy CI, Bell JT, Spector T, Baumbach J, O’Toole PW, Peters A, Haller D (2020) Arrhythmic gut microbiome signatures for risk profiling of Type-2 Diabetes. Cell Host Microbe. 2020 Aug 12;28(2):258-272.e6. (download from CellPress)

  26. Li W, Baumbach J, Larsen MJ, Mohammadnejad A, Lund J, Christensen K, Christiansen K, Tan Q. (2020) Differential long non-coding RNA profiling of body mass index in twins. Epigenomics 2020 Sep;12(17):1531-1541 (download from Future Medicine)

  27. Baumgarten N, Hecker D, Karunanithi S, Schmidt F, List M, Schulz MH. (2020) EpiRegio: analysis and retrieval of regulatory elements linked to genes. Nucleic Acids Res. 2020 Jul 2;48(W1):W193-W199. (download from Oxford Academic)

  28. Parise MTD, Parise D, Kato RB, Pauling JK , Tauch A, de Carvalho Azevedo VA, Baumbach J (2020) CoryneRegNet 7, the reference database and analysis platform for corynebacterial gene regulatory networks. Nat Sci Data. 2020 May 11;7(1):142. (download from Nature)

  29. Silverman EK, Schmidt HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Conte F, Di Costanzo A, Farina L, Fiscon G, Gatto L, Gentili M, Loscalzo J, Marchese C, Napoli C, Paci P, Petti M, Quackenbush J, Tieri P, Viggiano D, Vilahur G, Glass K, Baumbach J (2020) Molecular networks in Network Medicine: Development and applications. Wiley Interdiscip Rev Syst Biol Med. 2020 Apr 19;e1489. (download from Wiley Online Library).

  30. Blumenthal DB, Viola L, List M, Baumbach J, Tieri P, Kacprowski T. (2020) EpiGEN: an epistasis simulation pipeline. Bioinformatics. 2020 Apr 14;btaa 245 (download from Oxford Academic)

  31. Chondrogiannis T, Bouros B, Gamper J, Leser U, Blumenthal DB. (2020) Finding k-shortest paths with limited overlap. The VLDB Journal 29, 1023–1047 (2020). (download from Springer)

  32. Li Sh, Lund J, Christensen K, Baumbach J, Mengel-From J, Kruse T, Li W, Mohammadnejad A, Pattie A, Marioni R, Deary I, Tan Q. (2020) Exploratory analysis of age and sex dependent DNA methylation patterns on the X-chromosome in whole blood samples. Genome Med. 2020 Apr 28;12(1):39. (download from Genome Medicine)

  33. Stalidzans E, Zanin M, Tieri P, Castiglione F, Polster A, Scheiner S, Pahle J, Stres B, List M, Baumbach J, Lautizi M, Van Steen K, Schmidt HHHW. (2020) Mechanistic modeling and multiscale applications for precision medicine: theory and practice. Network and Systems Medicine 7 May, 2020, 3(1). (download from liebertpub)

  34. Mergner J, Frejno M, List M, Papacek M, Chen X, Chaudhary A, Samaras P, Richter S, Shikata H A, Messerer M, Lang D, Altmann S, Cyprys P, Zolg D P, Mathieson T, Bantscheff M, Hazarika R R, Schmidt T, Dawid C, Dunkel A, Hofmann T, Sprunck S, Falter-Braun P, Johannes F, Mayer K F X, Jürgens G, Wilhelm M, Baumbach J, Grill E, Schneitz K, Schwechheimer C, Kuster B. (2020) Mass-spectrometry-based draft of the Arabidopsis proteome. Nature 2020 Mar;579(7799):409-414. (download from Nature)

  35. Lund JB, Li S, Baumbach J, Christensen K, Li W, Mohammadnejad A, Pattie A, Marioni RE, Deary IJ, Tan Q. (2020) Weighted gene co-regulation network analysis (WGCNA) of promoter DNA methylation on all-cause mortality in old-aged birth cohorts finds modules of high-risk associated biomarkers. J Gerontol A Biol Sci Med Sci. 2020 Mar 10 pii: glaa066. (download from Oxford Academic)

  36. Scherer M, Nebel A, Franke A, Walter J, Lengauer T, Bock C, Müller F, List M. (2020) Quantitative Comparison of Within-Sample Heterogeneity Scores for DNA Methylation Data. Nucleic Acids Res. 2020 May 7;48(8):e46. (download from Oxford Academic)

  37. Wolff J, Pauling JK, Keck A, Baumbach J. (2020) Economic Impact Studies of Artificial Intelligence in Healthcare: A Systematic Review. J Med Internet Res 2020 Feb 20;22(2):e16866. (download from JMIR)

  38. Larsen SJ, Schmidt HHHW, Baumbach J. (2020) De novo and supervised endophenotyping using network-guided ensemble learning. Systems Medicine  3 (1): 8–21. (download from liebertpub)

​Before 2020​

​

  1. Elkjaer ML, Frisch T, Reynolds R, Kacprowski T, Burton M, Kruse TA, Thomassen M, Baumbach J, Illes ZL. (2019) Molecular signature of different lesion types in the brain white matter of patients with progressive multiple sclerosis. Acta Neuropathol. Commun. 2019 Dec 11;7(1):205. (download from BMC)

  2. Messerer K, Kacprowski T, Kolo H, Baumbach J, Knoke T. (2019) Importance of considering the growth response after partial harvesting and economic risk of discounted net revenues when optimizing uneven-aged forest management. Can. J. For. Res. 09.01.2020 10.1139/cjfr-2018-0546  (download from NRC Research Press)

  3. Salgado-Albarrán M, González-Barrios R, Guerra-Calderas L, Alcaraz N, Sánchez-Correa TS, Castro-Hernández C, Sánchez-Pérez Y, Aréchaga-Ocampo E, García-Carrancá A, Cantú de Léon D, Herrera L, Baumbach J, Soto-Reyes E. (2019) The epigenetic factor BORIS (CTCFL) controls the Androgen Receptor regulatory network in ovarian cancer. Oncogenesis 2019 Aug 12;8(8):41. (download from Nature)

  4. Li W, Zhang D, Wang W, Wu Y, Mohammadnejad A, Lund J, Baumbach J, Christiansen L, Tan Q. (2019) DNA methylome profiling in identical twin pairs discordant for body mass index. International Journal of Obesity. 2019 Dec;43(12):2491-2499. (download from Nature)

  5. do Canto LM, Larsen SJ, Catin Kupper BE, Begnami MDFS, Scapulatempo-Neto C, Petersen AH, Aagaard MM, Baumbach J, Aguiar S Jr, Rogatto SR. (2019) Increased levels of genomic instability and mutations in homologous recombination genes in locally advanced rectal carcinomas. Front Oncol. 2019 May 14;9:395. (download from Frontiers)

  6. Ward-Caviness CK, de Vries PS, Wiggins KL, Huffman JE, Yanek LR, Bielak LF, Giulianini F, Guo X, Kleber ME, Kacprowski T, Groß S, Petersman A, Davey Smith G, Hartwig FP, Bowden J, Hemani G, Müller-Nuraysid M, Strauch K, Koenig W, Waldenberger M, Meitinger T, Pankratz N, Boerwinkle E, Tang W, Fu YP, Johnson AD, Song C, de Maat MPM, Uitterlinden AG, Franco OH, Brody JA, McKnight B, Chen YI, Psaty BM, Mathias RA, Becker DM, Peyser PA, Smith JA, Bielinski SJ, Ridker PM, Taylor KD, Yao J, Tracy R, Delgado G, Trompet S, Sattar N, Jukema JW, Becker LC, Kardia SLR, Rotter JI, März W, Dörr M, Chasman D, Dehghan A, O'Donnell CJ, Smith NL, Peters A, Morrison AC. (2019) Mendelian randomization evaluation of causal effects of fibrinogen on incident coronary heart disease. PLoS One. 2019 May 10;14(5):e0216222 (download from PLoS One)

  7. da Costa AABA, do Canto LM, Larsen SJ, Ribeiro ARG, Stecca CE, Petersen AH, Aagaard MM, de Brot L, Baumbach J, Baiocchi G, Achatz MI,  Rogatto SR. (2019) Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes. BMC Cancer. 2019 May 6;19(1):422. (download from BMC)

  8. Kessler SM, Hosseini K, Hussein UK, Kim KM, List M, Schultheiß CS, Schulz MH, Laggai S, Jang KY, Kiemer AK. (2019) Hepatocellular Carcinoma and Nuclear Paraspeckles: Induction in Chemoresistance and Prediction for Poor Survival. Cell Physiol Biochem. April 2019;52(4):787-801. (download from Cell Physiol Biochem)

  9. Casasa AI, Hassana AA, Larsen SJ, Gomez-Rangel V, Elbatreek M, Kleikers PWM, Guney E, Egeae J, López MG, Baumbach J, Schmidt HHHW. (2019) From single drug targets to synergistic network pharmacology in ischemic stroke. Proc Natl Acad Sci U S A. Apr 2;116(14):7129-7136. (download from PNAS)

  10. Tweedell RE, Tao D, Hamerly T, Robinson TM, Larsen S, Grønning AGB, Norris AM, King JG, Law HCH, Baumbach J, Bergmann-Leitner ES, Dinglasan RR. (2019) The Selection of a Hepatocyte Cell Line Susceptible to Plasmodium falciparum Sporozoite Invasion That is Associated With Expression of Glypican-3. Front Microbiol. 2019 Feb 28;10:127. (download from Frontiers)

  11. Rauch A, Haakonsson AK, Madsen JGS, Larsen M, Forss I, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Röttger R, Baumbach J, Scheele C, Kassem M, Mandrup S. (2019) Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis. Nat Genet. 2019 Apr;51(4):716-727. (download from Nature)

  12. Wiwie C, Kuznetsova I, Mostafa A, Rauch A, Haakonsson A, Barrio-Hernandez I, Blagoev B, Mandrup S, Schmidt H, Pleschka S, Röttger R, Baumbach J. (2019) Time resolved systems medicine reveals viral infection modulating host targets. Systems Medicine. 2019 Mar. (download from Libertpub)

  13. Frost F, Kacprowski T, Rühlemann M, Bülow R, Kühn JP, Franke A, Heinsen FA, Pietzner M, Nauck M, Völker U, Völzke H, Aghdassi AA, Sendler M, Mayerle J, Weiss FU, Homuth G, Lerch MM. (2019) Impaired Exocrine Pancreatic Function Associates With Changes in Intestinal Microbiota Composition and Diversity. Gastroenterology. 2019 Mar;156(4):1010-1015. (download from Gastroenterology) 

  14. Naz K, Naz A, Ashraf ST, Rizwan M, Ahmad J, Baumbach J, Ali A. (2019) PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. BMC Bioinformatics. Mar 12;20(1):123. (download from BMC)

  15. Block I, Müller C, Sdogati D, Pedersen H, List M, Jaskot A, Syse SD, Hansen PL, Schmidt S, Christiansen H, Casella C, Olsen SB, Blomstrøm M, Riedel A, Thomassen M, Kruse T, Hansen SK, Kioschis P, Mollenhauer J. (2019) CFP suppresses breast cancer cell growth by TES-mediated upregulation of the transcription factor DDIT3. Oncogene. 38, 4560–4573 (2019). (download from Nature)

  16. Rauch A, Haakonsson AK, Madsen JGS, Larsen M, Forss I, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Röttger R, Baumbach J, Scheele C, Kassem M, Mandrup S. (2019) Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis. Nat Genet. 2019 Apr;51(4):716-727. (download from Nature)

  17. Lund JB, Li S, Christensen K, Mengel-From J, Soerensen M, Marioni RE, Starr J, Pattie A, Deary IJ, Baumbach J, Tan Q. (2019) Age-dependent DNA methylation patterns on the Y chromosome in elderly males. Aging Cell. 2020 Feb;19(2):e12907. (download from Wiley) 

  18. Lund JB, Li S, Baumbach J, Svane AM, Hjelmborg J, Christiansen L, Christensen K, Redmond P, Marioni RE, Deary IJ, Tan Q (2019). DNA methylome profiling of all-cause mortality in comparison with age-associated methylation patterns. Clin Epigenetics. 2019 Feb 8;11(1):23. (download from BMC)

  19. Li W, Baumbach J, Mohammadnejad A, Brasch-Andersen C, Vandin F, Korbel JO, Tan Q (2019) Enriched power of disease-concordant twin-case-only design in detecting interactions in genome-wide association studies. Eur J Hum Genet. 2019 Apr;27(4):631-636. (download from Eur J Hum Genet.)

  20. Saeed MT, Ahmad J, Baumbach J, Pauling J, Shafi A, Paracha RZ, Hayat A, Ali A. (2018) Parameter estimation of qualitative biological regulatory networks on high performance computing hardware. BMC Syst Biol. 2018 Dec 29;12(1):146. (download from BMC)

  21. Larsen S, Röttger R, Collado-Vides J, Harald S, Baumbach J. (2018) E. coli gene regulatory networks are inconsistent with gene expression data. Nucleic Acids Res. 2019 Jan 10;47(1):85-92. (download from Oxford Academic)

  22. Martin NA, Nawrocki A, Molnar V, Elkjaer ML, Thygesen  EK, Palkovits M, Acs P, Sejbaek  T, Nielsen HH,  Hegedus Z, Sellebjerg  F, Barbosa EGV, Alcaraz  N, Gallyas  F Jr, Svenningsen AF, Baumbach J, Lassmann H, Larsen MR, Illes Z (2018) Orthologous proteins of experimental de- and remyelination are differentially regulated in the CSF proteome of multiple sclerosis subtypes. PLoS One. 2018 Aug 16;13(8):e0202530. (download from PLoS One)

  23. Li W, Christiansen L, Hjelmborg J, Baumbach J, Tan Q. (2018) On the power of epigenome-wide association studies using a disease-discordant twin design. Bioinformatics. 2018 Dec 1;34(23):4073-4078.  (download from Oxford Academic)

  24. Mohammadnejad, A., Brasch-Andersen, C., Li, W., Haagerup, A., Baumbach, J., Tan, Q. (2018) A case-only genome-wide association study on gene-sex interaction in allergic rhinitis. Ann Allergy Asthma Immunol. 2018 Sep;121(3):366-367.e2. (download from Annals of Allergy, Asthma & Immunology)

  25. Larsen SL, do Canto LM, Rogatto SR, Baumbach J. (2018) CoNVaQ: a web tool for copy number variation-based association studies. 2018 May 18;19(1):369. BMC Genomics (download  from BMC)

  26. Hassan SS, Jamal SB, Radusky LG, Tiwari S, Ullah A, Ali J, Behramand de Carvalho PVSD, Shams R, Khan S, Figueiredo HCP, Barh D, Ghosh P, Silva A, Baumbach J, Röttger R, Turjanski AG, Azevedo VAC. (2018) The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets. Front Genet. 2018 Feb 13;9:44. (download from PMC)

  27. Baumbach J, Schmidt HHHW. (2018) The End of Medicine as We Know It: Introduction to the New Journal, Systems Medicine. Systems Medicine. 1(1). Mar 2018. 1-2.  (download from liebertpub)

  28. Wiwie C, Baumbach J, Röttger R. (2018) Guiding biomedical clustering with ClustEval. Nature Protocols 2018 Jun;13(6):1429-1444.  (download from Nature)

  29. Frost F, Kacprowski T, Rühlemann MC, Franke A, Heinsen F, Völker U, Völzke H, Aghdassi AA, Mayerle J, Weiss FU, Homuth G, Lerch MM. (2018) Functional abdominal pain and discomfort (IBS) is not associated with faecal microbiota composition in the general population. BMJ Gut. 2019 Jun;68(6):1131-1133.  (download from BMJ Gut). 

  30. Pietzner M, Kacprowski T, Friedrich N. (2018) Empowering thyroid hormone research in human subjects using OMICs-technologies. J Endocrino. 2018 Jul;238(1):R13-R29 (download from JOE)

  31. Zanin M, Chorbev I, Stres B, Stalidzans E, Vera J, Tieri P, Castiglione F, Groen D, Zheng D, Baumbach J, Schmid JA, Basilio J, Klimek P, Debeljak N, Rozman D, Schmidt HHHW. (2017) Community effort endorsing multiscale modeling, multiscale data science and multiscale computing for systems medicine. Brief Bioinform. 2019 May 21;20(3):1057-1062. (download from Oxford Academic)

  32. Jamal SB, Hassan SS, Tiwari S, Viana MV, Benevides LJ, Ullah A, Turjanski AG, Barh D, Ghosh P, Costa DA, Silva A, Röttger R, Baumbach J, Azevedo V. (2017) An Integrative in-silico Approach for Therapeutic Target Identification in the Human Pathogen Corynebacterium diphtheria. PLoS ONE. 2017 Oct 19;12(10):e0186401. (download from PLoS One)

  33. Alcaraz N, List M, Batra R, Vandin F, Ditzel HJ, Baumbach .J (2017) De novo pathway-based biomarker identification. Nucleic Acids Res. 2017 Sep 19;45(16):e151. (download from Oxford Academic)

  34. Demirci MDS, Baumbach J, Allmer J. (2017) On the performance of pre-microRNA detection algorithms. Nature Communications. 2017 Aug 24;8(1):330.  (download from Nature)

  35. Christensen AG, Ehmsen S, Terp MG, Batra R, Alcaraz N, Baumbach J, Noer JB, Moreira J, Leth-Larsen R, Larsen MR, Ditzel HJ. (2017) Elucidation of Altered Pathways in Tumor-Initiating Cells of Triple-Negative Breast Cancer: A Useful Cell Model System for Drug Screening. Stem Cells. 2017 Aug;35(8):1898-1912. (download from Wiley)

  36. Lund J, List M, Baumbach J. (2017) Interactive microbial distribution analysis using BioAtlas. Nucleic Acids Res. 3 July 2017, 45(W1, W509–W513). (download from Oxford Academic)

  37. Batra R, Alcaraz N, Gitzhofer K, Pauling J, Ditzel JH, Hellmuth M, Baumbach J, List M. (2017) On the performance of de novo pathway enrichment. Nature Systems Biology and Applications. Mar 3,3:6(2017). (download from Nature)

  38. Almeida D, Skov I, Lund J, Mohammadnejad A, Silva A, Vandin F, Tan Q, Baumbach J, Röttger R. (2016) Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing. J Integr Bioinform.  2016 Dec 18;13(4):294. (download from JIB)

  39. Almeida D, Skov I, Silva A, Vandin F, Tan Q, Röttger R, Baumbach J. (2016) Efficient detection of differentially methylated regions using DiMmeR. Bioinformatics, 2016 Oct 29. pii: btw657. (download from Oxford Academic)

  40. Sun P, Guo J, Winneburg R, Baumbach J. (2016) Drug repurposing by integrated literature mining and drug-gene-disease triangulation. Drug Discovery Today. 2016 Oct 22. pii: S1359-6446(16)30386-5. (download from ScienceDirect)

  41. List M, Elnegaard MP, Schmidt S, Christiansen H, Tan Q, Mollenhauer J, Baumbach J. (2016) Efficient Management of High-Throughput Screening Libraries with SAVANAH. J Biomol Screen. 2016 Oct 11. pii: 1087057116673607. (download from SAGE)

  42. Christiansen A,  Davidsen JR,  Titlestad I,  Vestbo J, Baumbach J. (2016) A systematic review of breath analysis and detection of volatile organic compounds in COPD. J Breath Res. 2016 August 31;10(3):034002. (download from IOP)

  43. List M, Schmidt S, Christiansen H, Rehmsmeier M, Tan Q, Mollenhauer J, Baumbach J. (2016) Comprehensive analysis of high-throughput screens with HiTSeekR. Nucleic Acids Res. 2016 Aug 19;44(14):6639-48. (download from Oxford Academic)

  44. List M, Alcaraz N, Dissing-Hansen M, Ditzel H, Mollenhauer J, Baumbach J. (2016) KeyPathwayMinerWeb: online multi-omics network enrichment. Nucleic Acids Res. 2016 Jul 8;44(W1):W98-W104. (download from Oxford Academic)

  45. Chen M, Baumbach J, Vandin F, Röttger R, Barbosa E, Dong M, Frost M, Christiansen L, Tan Q. (2016) Differentially methylated genomic regions in adult twin pairs discordant for birth-weight. Ann Hum Genet 2016 Mar;80(2):81-7. (download from Wiley)

  46. Alcaraz N, List M, Dissing-Hansen M, Rehmsmeier M, Tan Q, Mollenhauer J, Ditzel HJ, Baumbach J. (2016) Robust de novo pathway enrichment with KeyPathwayMiner 5. F1000Research 2016, 5:1531. (download from F1000Reserach)

  47. Zeng Y, Baumbach J, Barbosa E, Azevedo V, Zhang C, Koblizek M. (2016) Metagenomic evidence for the presence of phototrophic Gemmatimonadetes bacteria in diverse environments. Environ Microbiol Rep. 2016 Feb;8(1):139-49. (download from Wiley)

  48. ​Almeida D, Azevedo V, Silva A, Baumbach J. (2016) PetriScape - A plugin for discrete Petri net simulations in Cytoscape. J Integr Bioinform. 13(1):284, 2016. (download from IB)

  49. Malek M, Ibragimov R, Albrecht M, Baumbach J. (2016) CytoGEDEVO - Global alignment of biological networks with Cytoscape. Bioinformatics. 2016, 32 (8): 1259-1261. (download from Oxford Academic)

  50. Wiwie C, Baumbach J, Röttger R. (2015) Comparing the performance of biomedical clustering methods. Nature Methods. 2015 Nov;12(11):1033-8. (download from Nature)

  51. de Castro Soares S, Geyik H, Ramos R, Sa PH, Barbosa E, Baumbach J, Figueiredo HC, Miyoshi A, Tauch A, Silva A, Azevedo V. (2015) GIPSy: Genomic Island Prediction Software (2015) J Biotechnol. 2016 Aug 20;232:2-11. (download from ScienceDirect)

  52. Hauschild AC, Frisch T, Baumbach JI, Baumbach J. (2015) Carotta - Revealing Hidden Confounder Markers in Metabolic Breath Profiles. Metabolites 2015, 5(2), 344-363. (download from MDPI)

  53. Abreu VAC, Almeida S, Tiwari S, Hassan SS, Mariano D, Silva A, Baumbach J, Azevedo V, Röttger R. (2015) CMRegNet – An interspecies reference database for corynebacterial and mycobacterial regulatory networks. BMC Genomics 2015 Jun 11;16(1):452. (download from BMC)

  54. Obaid A, Ahmad J, Naz A, Awan FM, Paracha RZ, Tareen SHK, Anjum S, Raza A, Baumbach J, Ali A. (2015) Modeling and analysis of innate immune responses induced by the host cells against Hepatitis C Virus infection. Integr. Biol. 2015 May 11;7(5):544-59. (download from RSC)

  55. Vu D, Szoke S, Wiwie C, Baumbach J, Cardinali G, Röttger R, Robert V. (2014) Massive fungal biodiversity data re-annotation with multi-level clustering. Nature Sci Rep. 2014 Oct 30;4:6837. (download from Nature)

  56. Barbosa E, Roettger R, Hauschild AC, Azevedo V, Baumbach J. (2014) On the limits of computational functional genomics for bacterial lifestyle prediction. Brief Funct Genomics 2014 Sep;13(5):398-408. (download from Oxford Academic)

  57. Baumbach J, Röttger R. (2014) Computational Integrative Biology - On the joint analysis of diverse biological data sets. Integrative Biology 2014, 6, 1008-1009. (download from RSC)

  58. Alcaraz N, Pauling J, Batra R, Barbosa E, Junge A, Christensen AGL, Azevedo V, Ditzel HJ, Baumbach J. (2014) KeyPathwayMiner 4.0: Condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. BMC Syst Biol 2014 Aug 19;8(1):99. (download from BMC)

  59. List M, Schmidt S, Trojnar J, Thomas J, Thomassen M, Kruse TA, Tan Q, Baumbach J, Mollenhauer J. (2014) Efficient Sample Tracking With OpenLabFramework. Nature Sci Rep. 2014, 4 (4278). (download from Nature)

  60. Pauling J, Anne C, Batra R, Alcaraz N, Barbosa E, Martin RL, Beck H, Larsen R, Azevedo V, Ditzel HJ, Baumbach J. (2014) Elucidation of epithelial-mesenchymal transition-related pathways in a triple negative breast cancer cell line model by multi-omics interactome analysis. Integrative Biology 2014,6, 1058-1068. (download from RSC)

  61. Barbosa E, Aburjaile FF, Ramos RTJ, Carneiro AR, Le Loir Y, Baumbach J, Miyoshi A,  Silva A, Azevedo V. (2014) Value of a newly sequenced bacterial genome. World J Biol Chem.  2014 May 26;5(2):161-8 (download from WJBC)

  62. Peng S, Roettger R, Speicher N, Guo J, Baumbach J. (2014) Bi-Force – Large-scale bicluster editing and its application to gene expression data biclustering. Nucleic Acids Res. 2014 May 1;42(9):e78. (download from Oxford Academic)

  63. Smolinska A, Hauschild AC, Fijten R, Dallinga J, Baumbach J, van Schooten F. (2014) Current breathomics – A review on data pre-processing techniques and machine learning in metabolomics breath analysis. J Breath Res. 2014 Apr 8;8(2):027105. (download from IOPscience)

  64. Maurer F, Hauschild AC, Eisinger K, Baumbach J, Mayor A, Baumbach JI. (2014). MIMA – A software for analyte identification in MCC/IMS chromatograms by mapping accompanying GC/MS measurements. Int. J. Ion Mobil. Spec. 17(2):95-101, 2014. (download from Springer)

  65. Eckel SP, Baumbach J, Hauschild AC. (2014) On the importance of statistics in breath analysis - Hope or curse? J Breath Res. 2014 Mar;8(1):012001. (download from IOPscience)

  66. Baumbach J, Guo J, Ibragimov R. (2013) Covering Tree with Stars. J Comp Optm 2013, 1382-6905. (download from Springer)

  67. Zakharkina T, Heinzel E, Koczulla RA, Greulich T, Rentz K, Pauling JK, Baumbach J, Herrmann M, Grünewald C, Dienemann H, von Müller L, Bals R. (2013)  Analysis of the Airway Microbiota of Healthy Individuals and Patients with Chronic Obstructive Pulmonary Disease by T-RFLP and Clone Sequencing. PLoS ONE 8(7):e68302, 2013. (download from PLoS One)

  68. Hauschild AC, Kopczynski D, D'Addario M, Baumbach JI, Rahmann S, Baumbach J. (2013) Peak Detection Method Evaluation for Ion Mobility Spectrometry by using Machine Learning Approaches. Metabolites 2013, 3(2), 277-293. (download from MDPI) - Best paper award in the journal Metabolites, awarded in 2015 (download from BMC)

  69. Barh D, Gupta K, Jain N, Khatri G, León-Sicairos N, Canizalez-Roman A, Tiwari S, Verma A, Rahangdale S, Shah Hassan S, Rodrigues Dos Santos A, Ali A, Carlos Guimarães L, Thiago Jucá Ramos R, Devarapalli P, Barve N, Bakhtiar M, Kumavath R, Ghosh P, Miyoshi A, Silva A, Kumar A, Narayan Misra A, Blum K, Baumbach J, Azevedo V. (2013) Conserved host-pathogen PPIs. Integr. Biol. 2013 Mar;5(3):495-509. (download from RSC)

  70. Roettger R, Kalaghatgi P, Sun P, Soares DC, Azevedo V, Wittkop T, Baumbach J. (2013) Density Parameter Estimation for Finding Clusters of Homologous Proteins - Tracing Actinobacterial Pathogenicity Life Styles. Bioinformatics. 2013 Jan 15;29(2):215-22. (download from Oxford Academic)

  71. Jungwirth B, Sala C, Kohl T, Uplekar S, Baumbach J, Cole St, Pühler A, Tauch A. (2013) High-resolution detection of DNA binding sites of the global transcriptional regulator GlxR in Corynebacterium glutamicum. Microbiology. 2013 Jan;159(Pt 1):12-22. (download from Microbiology Research)

  72. Santos AR, Pereira VB, Barbosa E, Baumbach J, Pauling J, Roettger R, Turk MZ, Silva A, Miyoshi A, Azevedo V. (2013) Mature Epitope Density – A strategy for target selection based on immunoinformatics and exported prokaryotic proteins. BMC Genomics 2013, 14(Suppl 6):S4. (

  73. Hauschild AC, Schneider T, Pauling J, Rupp K, Jang M, Baumbach JI, Baumbach J. (2012) Computational methods for metabolomics data analysis of ion mobility  spectrometry data - Reviewing the state of the art. Metabolites 2012, 2, 733-755. (download from MDPI)

  74. Aslakson E, Szekely S, Vernon S, Bateman C, Baumbach J, Setty Y. (2012) Live Sequence Charts to Model Medical Information. Theor Biol Med Model. 2012 Jun 15;9(1):22. (download from BMC)

  75. Hauschild AD, Baumbach JI, Baumbach J. (2012) Integrated Statistical Learning of Metabolic Ion Mobility Spectrometry Profiles for Pulmonary Disease Identification. Genet Mol Res. 2012 Jul 10;11(AOP). (download from GMR)

  76. Roettger R, Rueckert R Taubert J, Baumbach J. (2012) How Little Do We Actually Know? -- On the Size of Gene Regulatory Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5): 1293-1300. (previously appeared in shorter form in the proceedings of the APBC 2012). (download from IEEE)

  77. Baumbach J. (2012) Integrative computational biology. Integr Biol. 2012, 4, 713-714. (download from Oxford Academic)

  78. Alcaraz N, Friedrich T, Koetzing T, Krohmer A, Mueller J, Pauling J, Baumbach J. (2012) Efficient key pathway mining - Combining networks and OMICS data. Integr Biol., 2012, 4 (7), 756 - 764. (download from Oxford Academic)

  79. Soares SC, Abreu V, McCulloch J, D'Afonseca V, Ramos RTJ, Silva AL, Ruiz JC, Baumbach J, Trost E, Tauch A, Hirata R, Mattos-Guaraldi AL, Miyoshi A, Azevedo V. (2012) PIPS - Pathogenicity Island Prediction Software. PLoS ONE 7(2): e30848. (download from PLoS One)

  80. Pauling J, Roettger R, Neuner A, Salgado H, Collado-Vides J, Tauch A, Puehler A, Baumbach J. (2012) On the trail of EHEC/EAEC - Unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria. Integr Biol., 2012, 4 (7), 728 - 733. (download from Oxford Academic)

  81. Pauling J, Roettger R, Tauch A, Azevedo V, Baumbach J. (2012) CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands. Nucleic Acids Res. 2012 Jan;40(1):D610-4. (download from Oxford Academic)

  82. Santos AR, Santos MA, McCulloch JA, Baumbach J, Oliveira GC, Silva AJ, Miyoshi A, Azevedo V. (2011) A singular value decomposition approach for improved taxonomy classification of biological sequences. BMC Genomics 2011, 12(Suppl 4):S11. (download from BMC)

  83. Wittkop T, Rahmann S, Roettger R, Boecker S, Baumbach J. (2011) Extension and robustness of Transitivity Clustering for protein-protein interaction network analysis. Int Math. 2011, 7:4, 255-273. (download from Tayler and Francis Online)

  84. Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. (2011) clusterMaker: A Multi-algorithm Clustering Plugin for Cytoscape. BMC Bioinformatics 2011 Nov 9;12(1):436. (download from BMC)

  85. Cerdeira LT, Carneir AR, Ramos RTJ, de Almeida SS, D'Afonseca V, Schneider MPC, Baumbach J, Andreas Tauch A, McCulloch JA, Azevedo VA, Silva A. (2011) Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study. J Microbiol Methods. 2011 Aug;86(2):218-23. (download from Science Direct)

  86. Ramos TRTJ, Carneiro AR, Baumbach J, Azevedo V, Schneider MPC, Silva A. (2011) Analysis of quality raw data of second generation sequencers with Quality Assessment Software. BMC Res Notes. 2011 Apr 18;4(1):130. (download from BMC)

  87. Ruiz JC, D'Afonseca V, Silva A, Ali A, Pinto AC, Santos AR, Rocha AA, Lopes DO, Dorella FA, Pacheco LG, Costa MP, Turk MZ, Seyffert N, Moraes PM, Soares SC, Almeida SS, Castro TL, Abreu VA, Trost E, Baumbach J, Tauch A, Schneider MP, McCulloch J, Cerdeira LT, Ramos RT, Zerlotini A, Dominitini A, Resende DM, Coser EM, Oliveira LM, Pedrosa AL, Vieira CU, Guimaraes CT, Bartholomeu DC, Oliveira DM, Santos FR, Rabelo EM, Lobo FP, Franco GR, Costa AF, Castro IM, Dias SR, Ferro JA, Ortega JM, Paiva LV, Goulart LR, Almeida JF, Ferro MI, Carneiro NP, Falcao PR, Grynberg P, Teixeira SM, Brommonschenkel S, Oliveira SC, Meyer R, Moore RJ, Miyoshi A, Oliveira GC, Azevedo V. (2011) Evidence for Reductive Genome Evolution and Lateral Acquisition of Virulence Functions in two Corynebacterium pseudotuberculosis strains. PLoS One. 2011 Apr 18;6(4):e18551(download from PLoS One)

  88. Wittkop T, Emig D, Truss A, Albrecht M, Boecker S, Baumbach J. (2011) Comprehensive cluster analysis with Transitivity Clustering. Nature Protocols 2011 Feb;6(3):285-95. (download from Nature)

  89. Alcaraz NM, Kucuk H, Weile J, Wipat A, Baumbach J. (2011) KeyPathwayMiner - Detecting case-specific biological pathways by using expression data. Int Math. 2011, 7:4, 299-313. (download from Tayler and Francis Online)

  90. Baumbach J. (2010) On the power and limits of evolutionary conservation - unraveling bacterial gene regulatory networks. Nucleic Acids Res. 2010 Dec 1;38(22):7877-84. (download from Oxford Academic)

  91. Krol E, Blom J, Winnebald J, Berhorster A, Barnett MJ, Goesmann A ,Baumbach J, Becker A. (2011) RhizoRegNet-A database of rhizobial transcription factors and regulatory networks. J Biotechnol. 2011 Aug 20;155(1):127-34. (download from Elsevier)

  92. Wittkop T, Emig D, Lange SJ, Rahmann S, Albrecht M, Morris JH, Boecker S, Stoye J, Baumbach J. (2010) Partitioning biological data with Transitivity Clustering. Nature Methods 2010 Jun;7(6):419-20. (download from Nature)

  93. Emig D, Salomonis N, Baumbach J, Lengauer T, Conklin BR, Albrecht M. (2010) AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res. 2010 Jul 1;38 Suppl:W755-62. (download from Oxford Academic)

  94. Baumbach J, Wittkop T, Kleindt CK, Tauch A. (2009) Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nature Protocols. 2009 Jun;4(6):992- 1005. (download from Nature)

  95. Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J. (2009) From Corynebacterium glutamicum to Mycobacterium tuberculosis - Towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. Nucleic Acids Res. 2009 Aug;37(14):e97. (download)

  96. Keilwagen J, Baumbach J, Kohl T, Grosse I. (2009) MotifAdjuster: A tool for computational reassessment of transcription factor binding site annotations. Genome Biol 2009 May 1;10(5):R46. (download from BMC)

  97. Baumbach J, Rahmann S, Tauch A. (2009) Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. BMC Syst Biol. 2009 Jan 15;3(1):8. (download from BMC)

  98. Baumbach J, Rahmann S, Tauch A. (2009) Towards the integrated analysis, visualization, and reconstruction of microbial gene regulatory networks. Brief Bioinform. 2009 Jan;10(1):75-83. (download from Oxford Academic)

  99. Kohl T, Baumbach J, Jungwirth B, Puehler A, Tauch A. (2008) The GlxR regulon of the amino acid producer Corynebacterium glutamicum: in silico and in vitro detection of DNA binding sites of a global transcription regulator. J Biotechnol. 31;135(4):340-350. (download from Elsevier)

  100. Baumbach J, Apeltsin L. (2008) Linking Cytoscape and the corynebacterial reference database CoryneRegNet. BMC Genomics. 2008 Apr 21;9(1):184. (download from BMC)

  101. Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hueser AT, Kalinowski J, Oehm S, Puehler A, Rahmann S, Weile J, Goesmann A. (2007) CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Syst Biol 1 (1):55. (download from BMC)

  102. Baumbach J. (2007) CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 2007, 8:429. (download from BMC)

  103. Wittkop T, Baumbach J, Lobo FP, Rahmann S. (2007) Large scale clustering of protein sequences with FORCE -- A layout based heuristic for weighted cluster editing. BMC Bioinformatics 2007, 8:396. (download from BMC)

  104. Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A. (2006) CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. J Biotechnol., 2007 Apr 30;129(2):279-289. (download from ScienceDirect)

  105. Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A. (2006) CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics. 2006 Feb 14;7(1):24. (download from BMC)

  106. Koehler J, Baumbach J, Taubert J, Specht M, Skusa A, Rueegg A, Rawlings C, Verrier P, Philippi S. (2006) Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. 2006 Mar 13;22(11):1383-1390. (download from Oxford Academic)

Conference proceedings

  1. Pustozerova A, Baumbach J, Mayer R (2023) Differentially Private Federated Learning: Privacy and Utility Analysis of Output Perturbation and DP-SGD. In 2023 IEEE International Conference on Big Data, Big Data, December, 2023, Sorrento, Italy.

  2. Pustozerova A, Baumbach J, Mayer R (2023) Analysing Utility Loss in Federated Learning with Differential Privacy. In International Conference on Trust, Security and Privacy in Computing and Communications, TrustCom, November 2023, Exeter, UK.

  3. Holzinger A, Saranti A, Hauschild AC, Beinecke J, Heider D, Roettger R, Mueller H, Baumbach J, Pfeifer B (2023) Human-in-the-Loop Integration with Domain-Knowledge Graphs for Explainable Federated Deep Learning. CD-MAKE 2023, Aug 22. (pp. 45-64). Springer Lecture Notes in Computer Science, vol 14065.

  4. Wolff J, Matschinske J, Baumgart D, Pytlik A, Keck A, Natarajan A, von Schacky CE, Pauling JK, Baumbach J (2022) Federated machine learning for a facilitated implementation of Artificial Intelligence in healthcare – a proof of concept study for the prediction of Coronary Artery Calcification Scores. J Integr Bioinform. 2022 Sep 05, 2022;pp. 20220032. (download from De Gruyter)

  5. Nasirigerdeh R, Torkzadehmahani R, Baumbach J, Blumenthal DB (2021) On the Privacy of Federated Pipelines. In Proceedings of the 44th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR ’21), July 11–15, 2021, Virtual Event, Canada. ACM, New York, NY, USA. https://doi.org/10.1145/3404835.3462996

  6. Sanchez CS, Wieder A, Sottovia P, Bortoli S, Baumbach J, Axenie C. (2020) GANNSTER: Graph-Augmented Neural Network Spatio-Temporal Reasoner
    for Traffic Forecasting. Proceedings of of the Joint European Conference on Machine Learning and Knowledge Discovery in Databases, ECML/PKDD, Sep. 14-18 2020, Ghent, Belgium (accepted)

  7. List M, Amirabad AD, Kostka D, Schulz MH. (2019) Large-scale inference of competing endogenous RNA network with sparse partial correlation ISMB/ECCB, Bioinformatics, 2019 Jul 15;35(14):i596-i604. (download from Oxford Academic)

  8. Sturm G, Finotello F, Petitprez F, Zhang JD, Baumbach J, Fridman WH, List M, Aneichyk T (2019) Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology. Proceedings of the Intelligent Systems for Molecular Biology, ISMB, Bioinformatics 2019 2019 Jul 15;35(14):i436-i445. (download from Oxford Academic)

  9. Schmidt F*, List M*, Cukuroglu E, Köhler S, Göke J, Schulz MH. (2018) An ontology-based method for assessing batch effect adjustment approaches in heterogeneous data sets. Proceedings of the European Conference on Computational Biology, ECCB, Sept. 9-12, 2018, Athens (Greece)
    Bioinformatics 2018, (download from Oxford Academic) (*joint first authors)

  10. Barbosa E, Röttger R, Hauschild AC, Castro Soares S, Böcker S, Azevedo V, Baumbach J. (2017) LifeStyle-Specific-Islands (LiSSI): Integrated Bioinformatics Platform for Genomic Island Analysis. J Integr Bioinform. 2017 Jul 5;14(2). (download from DeGruyter)

  11. Larsen SJ, Baumbach J. (2017) CytoMCS: a multiple maximum common subgraph detection tool for Cytoscape. J Integr Bioinform. 2017 Jul 21;14(2). (download from DeGruyter)

  12. Larsen SJ, Alkaersig FG, Ditzel HJ, Jurisica I, Alcaraz N, Baumbach J. (2016) A Simulated Annealing Algorithm for Maximum Common Edge Subgraph Detection in Biological Networks. Proceedings of the Genetic and Evolutionary Computation Conference 2016, GECCO, July 20-24, 2016, Denver, USA. 2016: 341-348. (download from ACM).

  13. List M, Franz M, Thomassen M, Kruse TA, Tan Q, Mollenhauer J, Baumbach J. (2015) OpenLabNotes - An Eletronic Laboratory Notebook Extension for OpenLabFramework. J Integr Bioinform. 2015 Oct 6;12(3):274. (download from JIB)

  14. List M, Block I, Pedersen ML, Christiansen H, Schmidt S, Thomassen M, Tan Q, Baumbach J, Mollenhauer J. (2014) Microarray R-based Analysis of Complex Lysate Experiments with MIRACLE. Proceedings of the European Conference on Computational Biology, ECCB, Sept 7-10 2014, Strassbourg (France). Bioinformatics 2014, 30 (17): i631-i638. (download from Oxford Academic)

  15. Baumbach J, Guo J, Sun P. (2014) Complexity of Dense Bicluster Editing Problems. Proceedings of the International Computing and Combinatorics Conference 2014, COCOON, August 2014, Atlanta, USA. Lecture Notes in Computer Science, Vol. 8591, 2014, pp 154-165. (download from Springer)

  16. List M, Hauschild AC, Tan Q, Kruse TA, Mollenhauer J, Batra R*, Baumbach J*. (2014) Classification of Breast Cancer Subtypes by combining Gene Expression and DNA Methylation Data. J Integr Bioinform. 11(2):236, 2014. (download from JIB) (* joint last author)

  17. Misirli G, Hallinan J, Roettger R, Baumbach J, Wipat A. (2014) BacillusRegNet: A transcriptional regulation database and analysis platform for Bacillus species. J Integr Bioinform. 11(2):244, 2014. (download from JIB)

  18. Baumbach J, Guo J, Ibragimov R. (2014) Multiple Graph Edit Distance - Simultaneous Topological Alignment of Multiple Protein-Protein Interaction Networks with an Evolutionary Algorithm. Proceedings of the Genetic and Evolutionary Computation Conference 2014, GECCO, July 2014, Vancouver, Canada. 277-284. (download from ACM)

  19. Baumbach J, Guo J, Ibragimov .R (2014) Compactness-Preserving Mapping on Trees. Proceedings of Annual Symposium on Combinatorial Pattern Matching, CPM, June 2014, Moscow, Russia. Lecture Notes in Computer Science. Volume 8486, 2014, pp 162-171. (download from Springer)

  20. Ibragimov R, Malek M, Guo J, Baumbach J. (2013) GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment. Proceedings of the German Conference on Bioinformatics, GCB, 2013, OpenAccess Series in Informatics, 34:68--79. (download from OASIC)​

  21. Ibragimov R, Guo J, Baumbach J. (2013) Neighborhood-Preserving Mapping between Trees. Proceedings of the Workshop on Algorithms and Data Structures, WASD, August 2013, Ontario, Canada. Lecture Notes in Computer Science. Volume 8037, 2013, pp 427-438. (download from Springer)

  22. Ibragimov R, Martens J, Guo J, Baumbach J. (2013) NABEECO: Biological Network Alignment with Bee Colony Optimization Algorithm. Proceedings of the Genetic and Evolutionary Computation Conference 2013, GECCO, July 2013, Amsterdam, Netherlands. GECCO (Companion) 2013: 43-44.  (download from ACM)

  23. ​Böcker S, Baumbach J. (2013) Cluster Editing. Proceedings of the Computability in Europe conference, CiE, July 2013, Milan, Italy. Lecture Notes in Computer Science. Volume 7921, 2013, pp 33-44. (download from Springer)

  24. Baumbach J, Guo J, Ibragimov R. (2013) Covering Tree with Stars. Proceedings of the International Computing and Combinatorics Conference 2013, COCOON, June 2013, Hangzhou, PR China. Lecture Notes in Computer Science. Vol. 7936, 2013, pp 373-384. (download from Springer)

  25. Sung P, Guo J, Baumbach J. (2013) BiCluE - Exact and Heuristic Algorithms for Weighted Bi-cluster Editing of Biomedical Data. Proceedings of the Great Lakes Bioinformatics Conferences 2013, GLBIO, May 2013, Pittsburg, USA. BMC Proc. 2013 Dec 20;7(Suppl 7):S9. (download from BMC)

  26. Schneider T, Hauschild AC, Baumbach JI, Baumbach J. (2013) An integrative clinical database and diagnostics platform for biomarker analysis in ion mobility spectra of human exhaled air. J Integr Bioinform. 2013 Apr 2;10(2):218. (download from JIB)

  27. Roettger R, Kreutzer C, Vu TD, Wittkop T, Baumbach J. (2012) Online Transitivity Clustering of Biological Data with Missing Values. Proceedings of the German Conference on Bioinformatics, GCB, 2012, OpenAccess Series in Informatics, 26:57-68. (download from OASIC)​

  28. ​​​​​Baumbach J, Friedrich T, Koetzing T, Kromer A, Mueller J, Pauling J. (2012) Efficient algorithms for extracting biological key pathways with global constraints. Proceedings of the Genetic and Evolutionary Computation Conference, GECCO 2012, 2012, 169-176. (download from ACM)

  29. ​Sun P, Guo J, Baumbach J. (2012) Integrated simultaneous analysis of different biomedical data types with exact weighted bi-cluster editing. J Integr Bioinform, 2012 Jul 17;9(2):197 (download from JIB).

  30. Roettger R, Rueckert R, Taubert J, Baumbach J. (2012) ​How Little Do We Actually Know? -- On the Size of Gene Regulatory Networks.​ Proceedings of the 10th Asian Pacific Bioinformatics Conference, APBC, Jan 2012, Melbourne, Australia (download from IEEE)

  31. ​Wittkop T, Rahmann S, Baumbach J. (2010) Efficient Online Transcription Factor Binding Site Adjustment by Integrating Transitive Graph Projection with MoRAine 2.0. J Integr Bioinform, 2008 Aug 25;5 (2). (download from JIB)

  32. Baumbach J, Wittkop T, Weile J, Kohl T, Rahmann S. (2008) MoRAine - A web server for fast computational transcription factor binding motif re-annotation. J Integr Bioinform, 5 (2) : 91, 2008 (download from JIB)

  33. Baumbach J, Bunkowski A, Lange S, Oberwahrenbrock T, Kleinboelting N, Rahmann S, Baumbach JI. (2007) IMS2 - An integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath. J Integr Bioinform, 4 (3) : 75, 2007 (download from JIB)

  34. ​Rahmann S, Wittkop T, Baumbach J, Martin M, Truss A, Boecker S. (2007) Exact and Heuristic Algorithms for Weighted Cluster Editing. In Proc. 6th CSB, volume 6 of Computational Systems Bioinformatics. Imperial College Press, 2007 (download from World Scientific)

  35. Baumbach J, Brinkrolf K, Wittkop T, Tauch A, Rahmann S. (2006) CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes. J Integr Bioinform, 3 (2) : 24, 2006. (download from JIB)

Book chapters

  1. Lazareva O, Lautizi M, Fenn A, List M, Kacprowski T, Baumbach J (2020) Multi-Omics Analysis in a Network Context. In: Wolkenhauer O. (eds) Systems Medicine: Integrative, Qualitative and Computational Approaches. Reference Module in Biomedical Sciences, vol 1, 2021, pp 224-233, Elsevier (download from ScienceDirect)

  2. Nogales C, Grønning AGB, Sadegh S, Baumbach J, Schmidt HHHW (2020) Network Medicine-Based Unbiased Disease Modules for Drug and Diagnostic Target Identification in ROSopathies. In: Handbook of Experimental Pharmacology. 2020 Aug 12. Springer, Berlin, Heidelberg.  (download from Springer)

  3. Sturm G, Finotello F, List M (2020) In Silico Cell-Type Deconvolution Methods in Cancer Immunotherapy. In: Boegel S. (eds) Bioinformatics for Cancer Immunotherapy. Methods in Molecular Biology, vol 2120. Spring Science, Humana, New York, NY (download from Oxford Academic)

  4. Sturm G, Finotello F, List M (2020) Immunedeconv: An R Package for Unified Access to Computational Methods for Estimating Immune Cell Fractions from Bulk RNA-Sequencing Data. In: Boggle S. (eds) Bioinformatics for Cancer Immunotherapy. Methods in Molecular Biology, vol 2120. Humana, New York, NY.(download from Springer)

  5. List M, Alcaraz N, Batra R (2019) De Novo Pathway-Based Classification of Breast Cancer Subtypes. In: Canzar S, Ringeling FR. (eds) Protein-Protein Interaction Networks: Methods and Protocols. Methods in Molecular Biology, vol 2074, pp 201-213. Spring Science, Humana Press, New York, NY (download from Springer)

  6. Alcaraz N, Hartebrodt A, List M (2019) De Novo Pathway Enrichment with KeyPathwayMiner. In: Canzar S, Ringeling FR. (eds) Protein-Protein Interaction Networks: Methods and Protocols. Methods in Molecular Biology, vol 2074, pp 181-199 Spring Science, Humana Press, New York, NY (download from Springer)

  7. Frisch T, Gøttcke J, Röttger R, Tan Q, Baumbach J (2018) DiMmer: Discovery of Differentially Methylated Regions in Epigenome-Wide Association Study (EWAS) Data. In: Mamitsuka H. (eds) Data Mining for Systems Biology. Methods in Molecular Biology, vol 1807, pp 51-62. Spring Science, Humana Press, New York, NY (download from Springer)

  8.  Lund J, Tan Q, Baumbach J (2018) Online Interactive Microbial Classification and Geospatial Distributional Analysis Using BioAtlas. In: Mamitsuka H. (eds) Data Mining for Systems Biology. Methods in Molecular Biology, vol 1807, pp 21-35. Spring Science, Humana Press, New York, NY (download from Springer)

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