Our publications

Journals

  1. 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)

  2. 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 bodymass index. International Journal of Obesity. 2019 May 31. (download from rdcu)

  3. Matos Do Canto L, Larsen SJ, Kupper BEC, de Souza Begnami MDF, Scapulatempo-Neto C, Petersen AH, Aagaard MM, Baumbach J, Aguiar-Jr S, S Rogatto SR (2019) Increased levels of genomic instability and mutations in homologous recombination genes in locally advanced rectal carcinomas. Frontiers in Oncology. 14 May 2019 (download from Frontiers)

  4. 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)

  5. 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 Cancer)

  6. Kessler SM, Hosseini K, Hussein UK, Kim KM, List M, Schultheiß CS, Schulz MH, Laggai S, Jang KY, Kiemer A K (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)

  7. 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)

  8. Frisch T, Elkjaer ML, Reynolds R, Michel TM, Kacprowski T, Burton M, Kruse TA, Thomassen M, Baumbach J, Illes Z. (2019) MS Atlas – A molecular map of brain lesion stages in progressive multiple sclerosis. bioRxiv. posted on March 24, 2019. doi: https://doi.org/10.1101/584920 (download from bioRxiv)

  9. 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

  10. 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 bioinformatics)

  11. 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. 1 Mar 2019 (download from liebertpub)

  12. 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)

  13. 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. 2019 Feb 12. [Epub ahead of print] (download from Nature)

  14. 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 Mar 4. (download from Nature)

  15. 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. 2019 Feb 21:e12907. [Epub ahead of print] (download from Wiley) 

  16. 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)

  17. 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 Jan 18. (download from Eur J Hum Genet.)

  18. 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)

  19. 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)

  20. 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).

  21. Mohammadnejad, A., Brasch-Andersen, C., Li, W., Haagerup, A., Baumbach, J., Tan, Q. (2018). A Case-only Genome-Wide Association Study on Gene-Sex Ann Allergy Asthma Immunol. 2018 Sep;121(3):366-367.e2. doi: 10.1016/j.anai.2018.07.001 (download from Annals of Allergy, Asthma & Immunology).

  22. 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. doi: 10.1093/bioinformatics/bty532 (download from Oxford Academic).

  23. 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. 02 June 2018. doi: 10.1136/gutjnl-2018-316502. (download from Gut). 

  24. Pietzner M, Kacprowski T, Friedrich N (2018) Empowering thyroid hormone research in human subjects using OMICs-technologies. Journal of Endocrinology, JOE-18 May 3, 2018, doi: 10.1530/JOE-18-0117. (download from JOE).

  25. Larsen SL, do Canto LM, Rogatto SR, Baumbach J (2018) CoNVaQ: a web tool for copy number variation-based association studies. BMC Genomics. 2018 May 18;19(1):369. doi: 10.1186/s12864-018-4732-8 PubMed (download  from PMC).

  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. PubMed (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. doi: 10.1089/sysm.2017.28999.jba (download from Mary Ann Liebert)

  28. Wiwie C, Baumbach J, Röttger R (2018) Guiding biomedical clustering with ClustEval. Nature Protocols 2018 Jun;13(6):1429-1444. doi: 10.1038/nprot.2018.038. Epub 2018 May 24.  (download from Nature protocol)

  29. 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. 2017 Dec 5. doi: 10.1093/bib/bbx160. PubMed (download from Oxford Press)

  30. 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. PubMed (download from PLoS)

  31. 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. PubMed (download from Oxford Press)

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

  33. 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. PubMed (download from Wiley)

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

  35. 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). PubMed (download from Nature press)

  36. 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. PubMed (download from JIB).

  37. 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. PubMed (download from ScienceDirect)

  38. 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. PubMed (download from SAGE)

  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. PubMed (download from Oxford Press)

  40. 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. PubMed (download from IOP)

  41. 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. PubMed (download from Oxford Press)

  42. 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. PubMed (download from Oxford Press)

  43. 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. PubMed (download from F1000)

  44. 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. PubMed (download from IB)

  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. PubMed (download from Wiley)

  46. 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. PubMed (download from Wiley)

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

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

  49. 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. 2015 Sep 12. pii: S0168-1656(15)30115-2. PubMed (download from ScienceDirect)

  50. 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)

  51. 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. PubMed (download from BMC)

  52. 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. PubMed (download from RSC)

  53. 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. PubMed (download from Nature Publishing Group)

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

  55. 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. PubMed (download from BMC)

  56. 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. PubMed (download from RSC)

  57. 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 5(2):161-168. PubMed (download from WJBC)

  58. 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. PubMed (download from Oxford Press)

  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). PubMed (download from Nature Publishing Group)

  60. 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)

  61. 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. PubMed (download from IOPscience)

  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. PubMed (download from Oxford Press)

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

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

  65. 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. PubMed (download from PLoS)

  66. 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. PubMed (download from BMC)

  67. 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. PubMed (download from MDPI) - Best paper award in the journal Metabolites, awarded in 2015 (link). 

  68. 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. PubMed (download from RSC)

  69. 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. PubMed (download from Oxford Press)

  70. 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. PubMed (download from SGM)

  71. 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. PubMed (download from MDPI)

  72. Baumbach J (2012) Integrative computational biology. Integr Biol. 2012, 4, 713-714. PubMed (download from RSC)

  73. 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. PubMed (download from BMC)

  74. 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). PubMed (download from GMR)

  75. 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). PubMed (download from IEEE)

  76. 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. PubMed (download from RSC)

  77. 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. PubMed (download from PLoS)

  78. 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. PubMed (download from RSC).

  79. 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. PubMed (download from Oxford Press)

  80. 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)

  81. 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. PubMed (download from BMC)

  82. 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. PubMed (download from BMC)

  83. 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)

  84. 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. PubMed (download from Nature Publishing Group)

  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. PubMed (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. PubMed (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. PubMed (download from PLoS)

  88. 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. PubMed (download from ScienceDirect)

  89. 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. PubMed (download from Oxford Journals)

  90. 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. PubMed (download from Nature Publishing Group)

  91. 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. PubMed (download from Oxford Journals)

  92. 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. PubMed (download from Oxford Journals)

  93. 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. PubMed (download from Nature Publishing Group)

  94. 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. PubMed (download from Genome Biology)

  95. 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. PubMed (download from BMC)

  96. 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. PubMed (download from Oxford Journals)

  97. 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. PubMed (download from Science Direct)

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

  99. 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. PubMed (download from BMC)

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

  101. 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. PubMed (download from BMC)

  102. 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. PubMed (download from ScienceDirect)

  103. 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. PubMed (download)

  104. 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. PubMed (download from Oxford Journals)   

Conference proceedings

  1. List M, Amirabad AD, Kostka D, Schulz MH (2019) Large-scale inference of competing endogenous RNA network with sparse partial correlation (ISMB/ECCB), July 21-25, 2019 (accepted)

  2. 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 (ISMB/ECCB), July 21-25, 2019 (accepted)

  3. 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 University Press) (*joint first authors)

  4. 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). PubMed (download from DeGruyter)

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

  6. 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).

  7. 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. PubMed (download from JIB)

  8. 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. PubMed (download from Oxford Press)

  9. 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)

  10. 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. PubMed (download from JIB) (* joint last author)

  11. 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. PubMed (download from JIB)

  12. 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)

  13. 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)

  14. ​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)​

  15. 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)

  16. ​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)

  17. ​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)

  18. ​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)

  19. ​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. PubMed

  20. ​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. PubMed (download from JIB)

  21. ​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)

  22. ​​​​​​​​​​​​​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)

  23. ​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. PubMed (download from JIB).

  24. ​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 (in press).​ PubMed (download from IEEE)

  25. ​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). PubMed (download from JIB)

  26. ​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. PubMed (download from JIB)

  27. ​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)

  28. ​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. PubMed (download from life Sciences Society)

  29. ​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. 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. Pubmed (download from Springer)

  2. 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. Pubmed (download from Springer)

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

  4. 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. Pubmed (download from Springer)

 

Chair of Experimental Bioinformatics

TUM School of Life Sciences Weihenstephan

Technical University of Munich

Tel: +49-8161-71-2136

E-Mail: exbio[a.t_))wzw.tum.de

Office: OG-L06