Verena Schuenemann*, Alexander Peltzer*, Beatrix Welte, Willem Paul van Pelt, Martyna Molak, Chuan-Chao Wang, Anja Furtwängler, Christian Urban, Ella Reiter, Kay Nieselt, Barbara Teßmann, Michael Francken, Katerina Harvati, Wolfgang Haak, Stephan Schiffels, and Johannes Krause
Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods
Nature Communications 8:15694 (2017): (doi: 10.1038/ncomms15694)

Knauf S, Gogarten J, Schuenemann V, De Nys H, Duex A, Strouhal M, Mikalova L, Bos K, Armstrong R, Batamuzi E, Chuma I, Davoust B, Diatta G, Fyumagwa R, Kazwala R, Keyyu J, Lejora I, Levasseur A, Liu H, Mayhew M, Mediannikov O, Raoult D, Wittig R, Roos C, Leendertz F, Smajs D, Nieselt K, Krause J, Calvignac-Spencer S
African Nonhuman Primates Are Infected With The Yaws Bacterium Treponema pallidum subsp. pertenue.
Preprint – bioRxiv (2017): (doi: 10.1101/135491)

Seitz A, Nieselt K
Improving ancient DNA genome assembly.
PeerJ 5 (2017): e3126 (doi: 110.7717/peerj.3126).

Huson D, Tappu R, Bazinet A, Xie C, Cummings M, Nieselt K, Williams R
Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads.
Microbiome, 2017, Volume 5, Number 1, Page 1 (doi: 10.1186/s40168-017-0233-2).


Hart ML, Rusch E, Kaupp M, Neselt K, Aicher WK.
Expression of desmoglein 2, desmocollin 3 and plakophilin 2 in placenta and bone marrow-derived mesenchymal stromal cells. Stem Cell Reviews and Reports (2017): 1-9.

Arora N, Schuenemann VJ, Jäger G, Peltzer A, Seitz A, Herbig A, Strouhal M, Grillová L, Sánchez-Busó L, Kühnert D, Bos KI, Rivero Davis L, Mikalová L, Bruisten S, Komericki P, French P, Grant PR, Pando MA, Gallo Vaulet L, Fermepin MR, Martinez A, Centurion Lara A, Giacani L, Norris SJ, Šmajs D, Bosshard PP, González-Candelas F, Nieselt K, Krause J, Bagheri HC.
Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster. Nature Microbiology 2:16245, (doi: 10.1038/NMICROBIOL.2016.245)

Maerz JK, Roncoroni LP, Goldeck D, Abruzzese T, Kalbacher H, Rolauffs B, DeZwart P, Nieselt K, Hart ML, Klein G, Aicher WK.
Bone marrow-derived mesenchymal stromal cells differ in their attachment to fibronectin-derived peptides from term placenta-derived mesenchymal stromal cells.
Stem Cell Research & Therapy 2016, 7:29 (doi: 10.1186/s13287-015-0243-6).

Fu Q, Posth C, Hajdinjak M, Petr M, Mallick S, Fernandes D, Furtwängler A, Haak W, Meyer M, Mittnik A, Nickel B, Peltzer A, Rohland N, Slon V, Talamo S, Lazaridis I, Lipson M, Mathieson I, Schiffels S, Skoglund P, Derevianko A, Drozdov Nm Slavinsky V, Tsybankov A, Cremonesi R, Mallegni F, Gély B, Vacca E, González Morales M R, Straus L G, Neugebauer-Maresch C, Teschler-Nicola M, Constantin S, Teodora Moldovan O, Benazzi S, Peresani M, Coppola D, Lari M, Ricci S, Ronchitelli A, Valentin F, Thevenet C, Wehrberger K, Grigorescu D, Rougier H, Crevecoeur I, Flas D, Semal P, Mannino M A, Cupillard C, Bocherens H, Conard N J, Harvati K, Moiseyev V, Drucker D G, Svoboda J, Richard M P, Caramelli D, Pinhasi R, Kelso J, Patterson N, Krause J, Pääbo S and Reich D.
The genetic history of Ice Age Europe Nature 2016, 534:200-205 (doi: 10.1038/nature17993).

Peltzer A, Jäger G, Herbig A, Seitz A, Kniep C, Krause J, Nieselt K.
EAGER: efficient ancient genome reconstruction. GenomeBiology 2016, 17:60 (doi: 10.1186/s13059-016-0918-z)


Mechler L, Herbig A, Paprotka K, Fraunholz M, Nieselt K, Bertram R.
A novel point mutation promotes growth phase-dependent daptomycin tolerance in Staphylococcus aureus. Antimicrobial Agents and Chemotherapy 2015, 59(9):5366-5376.

Bischler T, Hock ST, Nieselt K, Sharma CM.
Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori. Methods 2015, 86:89-101 (

Hennig A, Bernhard J, Nieselt K.
Pan-Tetris – an interactive visualization for Pan-genomes. BMC Bioinformatics 2015, Proceedings of the 5th Symposium on Biological Data Visualization (preliminary paper pdf file).

Wills PR, Nieselt K, McCaskill JS.
Emergence of Coding and its Specificity as a Physico-Informatic Problem. Origins of Life and Evolution of Biospheres 2015, 45(1-2):249-255 (doi: 10.1007/s11084-015-9434-5).

Singh P, Benjak A, Schuenemann VJ, Herbig A, Avanzi C, Busso P, Nieselt K, Krause J, Vera-Cabrera L, Cole ST.
Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis. PNAS 2015, 112(14):4459-4464 (doi:10.1073/pnas.1421504112).

Thomason MK, Bischler T, Eisenbart SK, Förstner KU, Zhang A, Herbig A, Nieselt K, Sharma CM, Storz G.
Global transcriptional start site mapping using dRNA-seq reveals novel antisense RNAs in Escherichia coli. J Bacteriol. 2015, 197(1):18-28 (doi:10.1128/JB.02096-14).

Fengler S, Spirer I, Neef M, Ecke M, Nieselt K, Hampp R.
A Whole-Genome Microarray Study of Arabidopsis thaliana Semisolid Callus Cultures Exposed to Microgravity and Nonmicrogravity Related Spaceflight Conditions for 5 Days on Board of Shenzhou 8. BioMed Research International 2015 (doi:10.1155/2015/547495).


Lechner S, Prax M, Lange B, Huber C, Eisenreich W, Herbig A, Nieselt K, Bertram R.
Metabolic and transcriptional activities of Staphylococcus aureus challenged with high-doses of daptomycin. International Journal of Medical Microbiology 2014, 304(8):931-940, ISSN 1438-4221 (doi:10.1016/j.ijmm.2014.05.008).

Bos KI, Jäger G, Schuenemann VJ, Vågene ÅJ, Spyrou MA, Herbig A, Nieselt K, Krause J.
Parallel detection of ancient pathogens via array-based DNA capture. Philosophical Transactions of the Royal Society of London B: Biological Sciences 2014, 370(1660) (doi:10.1098/rstb.2013.0375).

Bos KI, Harkins KM, Herbig A, Coscolla M, Weber N, Comas I, Forrest SA, Bryant JM, Harris SR, Schuenemann VJ, Campbell TJ, Majander K, Wilbur AK, Guichon RA, Wolfe Steadman DL, Cook DC, Niemann S, Behr MA, Zumarraga M, Bastida R, Huson D, Nieselt K, Young D, Parkhill J, Buikstra JE, Gagneux S, Stone AC, Krause J.
Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis. Nature 2014, 514:494–497 (doi:10.1038/nature13591).

Jäger G, Peltzer A, Nieselt K.
inPHAP: Interactive visualization of genotype and phased haplotype data. BMC Bioinformatics 2014, 15:200 (doi:10.1186/1471-2105-15-200).

Felka T, Ulrich C, Rolauffs B, Mittag F, Kluba T, DeZwart P, Ochs G, Bonin M, Nieselt K, Hart ML, Aicher WK.
Nitric oxide activates signaling by c-Raf, MEK, p-JNK, p38 MAPK and p53 in human mesenchymal stromal cells inhibits their osteogenic differentiation by blocking expression of Runx2. Journal of Stem Cell Research & Therapy 2014, 4:4 (doi:0.4172/2157-7633.1000195).

Schröder W, Bernhardt J, Marincola G, Klein-Hitpass L, Herbig A, Krupp G, Nieselt K, Wolz C.
Altering gene expression by aminocoumarins: the role of DNA supercoiling in Staphylococcus aureus. BMC Genomics 2014, 15:291 (doi:10.1186/1471-2164-15-291).

Mendum TA, Schuenemann VJ, Roffey S, Taylor GM, Wu H, Singh P, Tucker K, Hinds J, Cole ST, Kierzek AM, Nieselt K, Krause J, Stewart GR.
Mycobacterium leprae genomes from a British medieval leprosy hospital: towards understanding an ancient epidemic. BMC Genomics 2014, 15(1):270 (doi:10.1186/1471-2164-15-270).


Ulrich C, Rolauffs B, Abele H, Bonin M, Nieselt K, Hart M, Aicher W.
Low osteogenic differentiation potential of placenta-derived mesenchymal stromal cells correlates with low expression of the transcription factors Runx2 and Twist2. Stem Cells and Development 2013, 22(21):1-14 (doi:10.1089/scd.2012.0693).

Polatkan AC, Nieselt K.
Collact.Me: Conceptual Framework for Extracting Domain-Specific Content from Twitter. Proceedings – 2013 IEEE Third International Conference on Cloud and Green Computing CGC 2013, 313-320 (doi:10.1109/CGC.2013.56).

Herbig A, Nieselt K.
Non-coding RNA, Classification. In “Encyclopedia of Systems Biology” (Dubitzki W, Wolkenhauer 0, Cho KH, Yokota, H (eds)). Springer 2013:1532-1534.

Herbig A, Nieselt K.
Non-coding RNA, Prediction. In “Encyclopedia of Systems Biology” (Dubitzki W, Wolkenhauer 0, Cho KH, Yokota, H (eds)). Springer 2013:1534-1538.

Schünemann VJ, Singh P, Mendum TA, Krause-Kyora B, Jäger G, Bos KI, Herbig A,…, Nieselt K, Krause J.
Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae. Science 2013, 341(6142):179-183 (doi:10.1126/science.1238286).

Herbig A, Sharma CM, Nieselt K.
Automated transcription start site prediction for comparative transcriptomics using the SuperGenome. EMBnet.journal19 (doi:10.14806/ej.19.A.617).

Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM.
High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLoS Genet 2013, 9(5):e1003495 (doi:10.1371/journal.pgen.1003495).

Lehrmann A, Huber M, Polatkan AC, Pritzkau A, Nieselt K.
Visualizing dimensionality reduction of systems biology data. Data Mining and Knowledge Discovery 2013, 27(1):146-165 (doi:10.1007/s10618-012-0268-8).

Schuster CF, Park JH, Prax M, Herbig A, Nieselt K, Rosenstein R, Inouye M, Bertram R.
Characterization of a mazEF toxin-antitoxin homologue from Staphylococcus equorum. J Bacteriol. 2013, 195(1):115-125 (doi:10.1128/JB.00400-12).


Bos KI, Stevens P, Nieselt K, Poinar HN, DeWitte SN, Krause J.
Yersinia pestis: New Evidence for an Old Infection. PLOS ONE 2012, 7(11):e49803. (doi:10.1371/journal.pone.0049803).

Jäger G, Battke F, Nieselt K.
REVEAL—visual eQTL analytics. Bioinformatics 2012, 28(18):i542-i548 (doi:10.1093/bioinformatics/bts382).

Herbig A, Jäger G, Battke F, Nieselt K.
GenomeRing: alignment visualization based on SuperGenome coordinates. Bioinformatics 2012, 28(12):i7-i15 (doi:10.1093/bioinformatics/bts217).

Heinrich J, Vehlow C, Battke F, Jäger G, Weiskopf D, Nieselt K.
iHAT: interactive Hierarchical Aggregation Table for Genetic Association Data. BMC Bioinformatics 2012, 13(Suppl 8):S2 (doi:10.1186/1471-2105-13-S8-S2).

Bartlett CW, Cheong SY, Hou L, Paquette J, Lum PY, Jäger G, Battke F, Vehlow C, Heinrich J, Nieselt K, Sakai R, Aerts J, Ray WC.
An eQTL biological data visualization challenge and approaches from the visualization community. BMC Bioinformatics 2012, 13(Suppl. 8):S8 (doi:10.1186/1471-2105-13-S8-S8).

Thomas L, Hodgson DA, Wentzel A, Nieselt K, Ellingsen TE, Moore J, Morrissey ER, Legaie R, The STREAM Consortium, Wohlleben W, RodrÍguez-García A, Martín JF, Burroughs NJ, Wellington EMH, Smith MCM.
Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture. Molecular and Cellular Proteomics 2012, 11(2):M111 (doi:10.1074/mcp.M111.013797).

Albrecht T, Raue S, Rosenstein R, Nieselt K, Götz F.
Phylogeny of the Staphylococcal Major Autolysin and Its Use in Genus and Species Typing. Journal of bacteriology 2012, 194(10):2630-2636 (doi:10.1128/JB.06609-11).

Martin JF, Santos-Beneit F, Rodriguez-Garcia A, Sola-Landa A, Smith MCM, Ellingsen TE, Nieselt K, Burroughs NJ, Wellington EMH.
Transcriptomic studies of phosphate control of primary and secondary metabolism in Streptomyces coelicolor. Applied Microbiology and Biotechnology 2012, 95(1):61-75 (doi:10.1007/s00253-012-4129-6).


Waldvogel E, Herbig A, Battke F, Nentwich M, Nieselt K, Ellingsen TE, Wentzel A, Hodgson DA, Wohlleben W, Mast Y.
The PII protein GlnK is a pleiotropic regulator for morphological differentiation and secondary metabolism in Streptomyces coelicolor. Appl Microbiol Biotechnol. 2011, 92(6):1219-36 (doi:10.1007/s00253-011-3644-1).

Spangenberg L, Battke F, Grana M, Nieselt K, Naya K.
Identifying associations between amino acid changes and meta information in alignments. Bioinformatics 2011, 27(20):2782-2789 (doi:10.1093/bioinformatics/btr476).

Battke F, Symons S, Herbig A, Nieselt K.
GaggleBridge – Collaborative data analysis. Bioinformatics 2011, 27(18):2612-2613 (doi:10.1093/bioinformatics/btr429).

Jäger G, Battke F, Nieselt K.
TIALA – Time Series Alignment Analysis. IEEE Symposium on Biological Data Visualization (BioVis symposium) 2011, IEEE Digital library, pp. 55-61.

Vehlow C, Heinrich J, Battke F, Weiskopf D, Nieselt K.
iHAT: the interactive Hierarchical Aggregation Table. IEEE Symposium on Biological Data Visualization (BioVis symposium) 2011, IEEE Digital library, pp. 63-69 (doi:10.1186/1471-2105-13-S8-S8).

Symons S, Nieselt K.
MGV: A Generic Graph Viewer for Comparative Omics Data. Bioinformatics. 2011, 27(16):2248-55 (doi:10.1093/bioinformatics/btr351).

Battke F, Nieselt K.
Mayday SeaSight: Combined Analysis of Deep Sequencing and Microarray Data. PLoS ONE 2011, 6(1): e16345 (doi:10.1371/journal.pone.0016345).

D’Alia D, Eggle D, Nieselt K, Hu W-S, Breitling R, Takano E.
Deletion of the signaling molecule synthase ScbA has pleiotropic effects on secondary metabolite biosynthesis, morphological differentiation and primary metabolism Streptomyces coelicolor A3(2). Microbial Biotechnology 2011, 4(2):239-251 (doi:10.1111/j.1751-7915.2010.00232.x).

Herbig A, Nieselt K.
nocoRNAc: Characterization of non-coding RNAs in prokaryotes. BMC Bioinformatics 2011, 12:40 (doi:10.1186/1471-2105-12-40).

Löffler M., Zieker D., Weinreich J., Löb S., Königsrainer I., Symons S., Bühler S., Königsrainer A., Northoff H., Beckert S.
Wound fluid lactate concentration: a helpful marker for diagnosing soft-tissue infection in diabetic foot ulcers? Preliminary findings. Diabetic Medicine 2011, 28(2):175-8 (doi:10.1111/j.1464-5491.2010.03123.x).


Sommer JU, Schmitt A, Heck M, Schaeffer EL, Fendt M, Zink M, Nieselt K, Symons, S, Petroianu G, Lex A, Herrera-Marschitz M, Spanagel R, Falkai P, Gebicke-Haerter PJ.
Differential expression of presynaptic genes in a rat model of postnatal hypoxia: relevance to schizophrenia. European archives of psychiatry and clinical neuroscience 2010, 260:81-89 (doi:10.1007/s00406-010-0159-1).

Nieselt K, Kaufmann M, Gerasch A, Lenhof H-P, Spehr M, Hesse S, Gumhold S.
Visuelle Analytik biologischer Daten. Informatik Spektrum, 2010, 33(6):559-568 (doi:10.1007/s00287-010-0482-y).

Battke F, Körner S, Hüttner S, Nieselt K.
Efficient sequence clustering for RNA-seq data without a reference genome. German Conference Bioinformatics 2010. Lecture Notes in Informatics. Proceedings of the German Conference on Bioinformatics 2010, Vol P-173, 21-30.

Battke F, Symons S, Nieselt K.
Mayday – Integrative Analytics for Expression Data. BMC Bioinformatics 2010, 11:121 (doi:10.1186/1471-2105-11-121).

Symons S, Zipplies C, Battke F, Nieselt K.
Integrative Systems Biology Visualization with MAYDAY. Journal of Integrative Bioinformatics 2010, 7(3):115 (doi:10.2390/biecoll-jib-2010-115).

Alam MT, Merlo ME, STREAM Consortium, Hodgson DA, Wellington EM, Takano E, Breitling R.
Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. BMC Genomics. 2010, 11:202 (doi:10.1186/1471-2164-11-202).

Zieker D, Königsrainer I, Tritschler I, Löffler M, Beckert S, Traub F, Nieselt K, Bühler S, Weller M, Gaedcke J, Taichman RS, Northoff H, Brücher BL, Königsrainer A.
Phosphoglycerate kinase 1 a promoting enzyme for peritoneal dissemination in gastric cancer. Int J Cancer. 2010, 126(6):1513-20 (doi:10.1002/ijc.24835).

Battke F, Herbig A, Wentzel A, Jakobsen O, Bonin M, Hodgson D, Wohlleben W, Ellingsen T, SysMO Stream Consortium, Nieselt K.
A Technical Platform for Generating Reproducible Expression Data from Streptomyces Coelicolor Batch Cultivations. In: Software Tools and Algorithms for Biological Systems. Springer (book series, Advances in Experimental Medicine and Biology), 2010.

Nieselt K, Battke F, Herbig A, et al.
The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics 2010, 11(1):10 (doi:10.1186/1471-2164-11-10).

D’Alia D, Nieselt K, Steigele S, Müller J, Verburg I, Takano E.
Non-coding RNA of glutamine synthetase I modulates antibiotic production in Streptomyces coelicolor A3(2). J Bacteriol 2010, 192(4):1160-4 (doi:10.1128/JB.01374-09).


Nieselt K, Dietzsch J, Heinrich J, Pritzkau A, Mosisch M, Bartz D.
Visuelle Analytik für Genexpressionsdaten. Datenbank-Spektrum 2009, 31(9):26-32.

Dietzsch J, Heinrich J, Nieselt K, Bartz D.
SpRay: A Visual Analytics Approach for Gene Expression Data. IEEE Symposium on Visual Analytics Science and Technology (VAST) 2009 (doi:10.1109/VAST.2009.5333911).

Gehlenborg N, Yan W, Lee IY, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L.
Prequips – An Extensible Software Platform for Integration, Visualization and Analysis of LC-MS/MS Proteomics Data. Bioinformatics 2009, 25(5):682-3 (doi:10.1093/bioinformatics/btp005).

Pfannenberg C, Königsrainer I,Aschoff P, Öksüz M, Zieker D, Beckert S, Symons S, Nieselt K, Glatzle J, v. Weyhern C, Brücher BL, Claussen CD, Königsrainer A.
F-FDG-PET/CT to Select Patients with Peritoneal Carcinomatosis for Cytoreductive Surgery and Hyperthermic Intraperitoneal Chemotherapy. Ann Surg Oncol. 2009, 16(5):1295-303 (doi:10.1245/s10434-009-0387-7).


Northoff H, Symons S, Zieker D, Schaible EV, Schäfer K, Thoma S, Löffler M, Abbasi A, Simon P, Niess AM, Fehrenbach E.
Gender- and menstrual phase dependent regulation of inflammatory gene expression in response to aerobic exercise. Exerc Immunol Rev. 2008;14:86-103.

Symons S, Weber K, Bonin M, Nieselt K.
ResqMi – a versatile algorithm and software for resequencing microarrays. German Conference Bioinformatics 2008. Lecture Notes in Informatics. In A. Beyer and M. Schroeder, editors, Proceedings of the German Conference on Bioinformatics 2008, pp 10-20.

Battke F, Müller-Tidow C, Serve H, Nieselt K.
Post-Hybridization Quality Measures for Oligos in Genome-Wide Microarray Experiments. 8th International Workshop on Algorithms in Bioinformatics (WABI). Proceedings (Lecture Notes in Computer Science), Subseries: Lecture Notes in Bioinformatics , Vol. 5251 Crandall, Keith A.; Lagergren, Jens (Eds.), pp 64-75.

Zieker D, Schäfer R, Glatzle J, Nieselt K, Coerper S, Northoff H, Königsrainer A, Hunt TK, Beckert S.
Lactate modulates gene expression in human mesenchymal stem cells. Langenbecks Arch Surg. 2008, 393(3):297-301 (doi:10.1007/s00423-008-0286-6).

Zieker D, Königsrainer, I, Traub T, Nieselt K, Knapp B, Schillinger C, Stirnkorb C, Stein H, Northoff H, Kupka S, Brücher B, Königsrainer A.
PGK1 a Potential Marker for Peritoneal Dissemination in Gastric Cancer. Cell Physiol Biochem. 2008, 21(5-6):429-36 (doi:10.1159/000129635).


Hömme C, Peerzada A, Behre G, Wang Y, McClelland M, Nieselt K, Zschunke M, Disselhoff C, Agrawa S, Isken F, Tidow N, Berdel W, Serve H, Müller-Tidow C.
Chromatin modifications induced by PML-RARalpha repress critical targets in leukemogenesis as analyzed by ChIP-chip. Blood 2008, 111(5):2887-95 (doi:10.1182/blood-2007-03-079921).

Altug-Teber Ö, Bonin M, Mau-Holzmann UA, Dufke A, Stappert H, Tekesin I, Heilbronner H, Nieselt K, Riess O.
Specific transcriptional changes in human fetuses with autosomal trisomies. Cytogenetic and Genome Research 2007; 119:171-184 (doi:10.1159/000112058).

Steigele S, Huber W, Stocsits C, Stadler PF, Nieselt K.
Comparative Analysis of Structured RNAs in S. cerevisiae indicates a Multitude of Different Functions.BMC Biology 5:25 (doi:10.1186/1741-7007-5-25).

Baum O, Ganster M, Baumgartner I, Nieselt K, Djonov V.
Basement membrane remodeling in skeletal muscles of patients with limb ischemia involves regulation of matrix metalloproteinases and tissue inhibitor of matrix metalloproteinases. J Vasc Res 2007;44:202-213.

Zieker J, Zieker D, Jatzko A, Dietzsch J, Nieselt K, Schmitt A, Bertsch T, Fassbender K, Spanagel R, Northoff H, Gebicke-Haerter PJ.
Differential gene expression in peripheral blood of patients suffering from post-traumatic stress disorder. Mol Psychiatry. 2007 Feb;12(2):116-8.


Markowitz S, Drummond A, Nieselt K, Wills PR.
Simulation model of Prebiotic Evolution of Genetic Coding. ALIFEX – Tenth International Conference on the Simulation and Synthesis of Living Systems.

Dietzsch J, Gehlenborg N, Nieselt K.
Mayday – a Microarray Data Analysis Workbench. Bioinformatics 22(8):1010-1012, 2006. For supplemental material for the paper click here.

Schütz CS, Kurek R, Bonin M, Clare SE, Nieselt K, Sotlar K, Fehm T, Solomayer E, Riess O, Wallwiener D, Neubauer H. Progression-specific Genes Identified by Expression Profiling of Matched Ductal Carcinomas in situ and Invasive Breast Tumors, Combining Laser Capture Microdissection and Oligonucleotide Microarray Analysis. Cancer Research 66(10):5278-5286, 2006.

Lehmann KA, Kaufmann M, Steigele S, Nieselt, K.
On the maximal cliques in c-max-tolerance graphs and their application in clustering molecular sequences. Algorithms Mol Biol. 1(1):9, 2006 (doi:10.1186/1748-7188-1-9).


Zieker D, Zieker J, Dietzsch J, Burnet M, Northoff H, Fehrenbach E.
cDNA-microarray analysis as a research tool for expression profiling in human peripheral blood following exercise. Exerc Immunol Rev. 2005;11:86-96.

Zieker D, Fehrenbach E, Dietzsch J, Fliegner J, Waidmann M, Nieselt K, Gebicke-Haerter P, Spanagel R, Simon P, Niess A, Northoff, H.
cDNA microarray analysis reveals novel candidate genes expressed in human peripheral blood following exhaustive exercise. Physiol Genomics 23:287-294, 2005.

Steigele S, Nieselt K.
Open Reading Frames provide a rich pool of potential Natural Antisense Transcripts in Fungal Genomes. Nucleic Acids Research 33(16):5034-5044, 2005.

Gehlenborg N, Dietzsch J, Nieselt K.
A Framework for Visualization of Microarray Data and Integrated Meta Information. Information Visualization. 2005. Special issue “Bioinformatics Visualization” Vol. 4(3):164-175.

Henz S, Huson D, Auch A, Nieselt-Struwe K, Schuster S.
Whole-genome prokaryotic phylogeny. Bioinformatics 2005, 21(10):2329-2335.


Schmollinger M, Nieselt K, Kaufmann M, Morgenstern B.
DIALIGN P: Fast pair-wise and multiple sequence alignment using parallel processors. BMC Bioinformatics 2004, 5:128 (doi:10.1186/1471-2105-5-128).

Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, Dietzsch J, Steigele S, Do H-H, Weiss G, Enard W, Heissig F, Arendt T, Nieselt-Struwe K., Eichler E, Pääbo S.
Regional Patterns of Gene Expression in Human and Chimpanzee Brains. Genome Research 14:455-460, 2004.


Bryant D, Huson D, Klöpper T, Nieselt-Struwe, K.
Distance corrections on recombinant sequences. Algorithms in Bioinformatics: Third International Workshop, WABI 2003. Proceedings (Lecture Notes in Computer Science, 2812), Benson, G. and Page, R. (Eds).

Henz S, Auch A, Huson D, Nieselt-Struwe K, Schuster S.
Whole Genome-Based Prokaryotic Phylogeny. Short paper at ECCB 2003.


Enard W, Khaitovich P, Klose J, Zöllner S, Heissig F, Giavalisco P, Nieselt-Struwe K, Muchmore E, Varki A, Ravid R, Doxiadis GM, Bontrop RE, Pääbo S.
Intra- and Inter-Specific Variation of Primate gene Expression Patterns. Science 2002, 296:340-343.


Nieselt-Struwe K, von Haeseler A.
Quartet-mapping, a generalization of the likelihood-mapping procedure. Molecular Biology and Evolution 2001, 18:1204-1219.


Bosse A, Stoykova A, Nieselt-Struwe K, Chowdhury K, Copeland NG, Jenkinds NA, Gruss P.
Identification of a Novel Mouse Iroquois Homeobox Gene, Irx5, and Chromosomal Localisation of All Members of the Mouse Iroquois Gene Family, Dev. Dynamics 2000, 218:160-174.

Nieselt-Struwe K.
Von der Quasispezies zum Hyperzyklus – ein Abriss der Eigenschen Evolutionstheorie. In: Auf den Spuren der Evolution, Michael Fasterding (Hrsg.), Edition Archaea.


Nieselt-Struwe K.
From likelihood-mapping to quartet-mapping, a new sequence analysis tool, In: Proceedings of the Trinational Workshop on Molecular Evolution, M.K. Uyenoyama und A. von Haeseler (Hrsg.), Duke University Publication Group, Duke University, Durham, North Carolina, 13-22, 1998.


Nieselt-Struwe K.
Graphs in Sequence Spaces: a Review of Statistical Geometry. Biophysical Chemistry 1997, 66:111-131.

Wills PR, Nieselt-Struwe K, Henderson L.
The Evolution of Genetic Coding. New Zealand BioScience 1997, 5:7-10.

Nieselt-Struwe, Wills PR.
The Emergence of Genetic Coding in Physical Systems. Journal of Theoretical Biology 1997, 187:1-14.

Plikat U, Nieselt-Struwe K, Meyerhans A.
Genetic Drift Can Dominate Short-Term Human Immunodeficiency Virus Type 1 nef Quasispecies Evolution In Vivo. Journal of Virology 1997, 71:4233-4240.


Nieselt-Struwe-K, Eigen M.
Vergleichende Sequenzanalysen von Virusgenen. In: Mathematik in der Praxis. Fallstudien aus Industrie, Wirtschaft, Naturwissenschaften und Medizin (Bachem, A., Jünger, M., Schrader, R., Hrg.). Springer-Verlag, 291-314, 1995.


Kuiken C, Nieselt-Struwe K, Weiler GTF, Goudsmit J.
Quasispecies Behaviour of Human Immunodeficiency Virus Type 1: Sample Analysis of Sequence Data. In: METHODS IN MOLECULAR GENETICS, Vol. 4, Molecular Virology Techniques, Part A. (Adolph, K.W., Editor). Academic Press, 100-119. 1994.


Schubert FR, Nieselt-Struwe K, Gruss P.
The Antennapedia-type Homeobox Genes have evolved from three Precursors separated early in Metazoan Evolution. Proc. Natl. Acad. Sci. USA 1993, 90:143-147.


Kreutz R, Dietrich U, Kühnel H, Nieselt-Struwe K, Eigen M, Rübsamen-Waigmann H.
Analysis of the Envelope Region of the Highly Divergent HIV-2ALT Isolate Extends the Known Range of Variability Within the Primate Immunodeficiency Viruses. AIDS Res. Human Retroviruses 1992, 8:1619-1629.

Nieselt-Struwe K.
Konfigurationsanalysen kombinatorischer und biologischer Optimierungsprobleme. Dissertation, Universität Bielefeld, 1992.


Eigen M, Nieselt-Struwe K.
How Old is the Immunodeficiency Virus? AIDS 1991, 4 (Suppl. 1):85-34.


Kirchhoff F, Jentsch KD, Bachmann B, Stuke A, Laloux C, Lüke W, Stahl-Hennig C, Schneider J, Nieselt-Struwe K, Eigen M, Hunsmann G.
A Novel Proviral Clone of HIV-2: Biological and Phylogenetic Relationship to Other Primate Immunodeficiency Viruses. Virology 1990, 177:305-311.

Technical Reports

Symons S, Nieselt K.
Data Mining Microarray Data – Comprehensive Benchmarking of Feature Selection and Classification Methods. For the technical report click here, for supplemental material for the paper click here.




Nieselt K.
New algorithmic and visualisation approaches to comparative genomics and transcriptomics. Votrag an der Universität Halle


Nieselt K.
Mayday and beyond: New Approaches for the Visualisation of Genomics and Transcriptomics Data. Keynote-Vortrag auf dem Symposium “Biological data Visualization – the art of presenting data in Gent, Belgium


Battke F, Symons S, Nieselt K.
Mayday RLink – The best of two worlds. Presentation at UseR! 2009. For an abstract click here.