Alina Hoffmann, ..., Kay Nieselt, Theresa Harbig, ..., and Gabriele Bierbaum
The unusual mode of action of the polyketide glycoside antibiotic cervimycin C 
mSphere

S. Zabel, P. Hennig and K. Nieselt
VIPurPCA: Visualizing and Propagating Uncertainty in Principal Component Analysis
IEEE Transactions on Visualization & Computer Graphics, vol. , no. 01, pp. 1-13, 5555. doi: 10.1109/TVCG.2023.3345532

Detert, K.,  Währer, J.,  Nieselt, K. &  Schmidt, H.
Broad time-dependent transcriptional activity of metabolic genes of E. coli O104:H4 strain C227/11Φcu in a soil microenvironment at low temperature. 
Environmental Microbiology Reports, 2023, 1–15, https://doi.org/10.1111/1758-2229.13198

Rhythm Shukla, ... Theresa Harbig, ... Kay Nieselt, ... Tanja Schneider, Markus Weingarth,
An antibiotic from an uncultured bacterium binds to an immutable target,
Cell, 2023, https://doi.org/10.1016/j.cell.2023.07.038.

Wolfgang Fuhl, Susanne Zabel, Kay Nieselt
Improving Taxonomic Classification with Feature Space Balancing 
Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad092, https://doi.org/10.1093/bioadv/vbad092

Zabel, S., Müller, J., Götz, F., & Nieselt, K.
BLASTphylo: An Interactive Web Tool for Taxonomic and Phylogenetic Analysis of Prokaryotic Genes.
Journal of Computational Biology, 30(9), 999-1008.

Harbig T, Witte Paz M, Nieselt K. 
GO-Compass: Visual Navigation of Multiple Lists of GO terms
Computer Graphics Forum 2023, 42(3) (https://doi.org/10.1111/cgf.14829)

Harbig T, Fratte J, Krone M, Nieselt K.
OmicsTIDE: interactive exploration of trends in multi-omics data

Bioinformatic Advances 2023, 3(1):1-8 doi.org/10.1093/bioadv/vbac093

Krauss S, Harbig TA, Rapp J, Schaefle T, Franz-Wachtel M, Reetz L, Elsherbini AMA, Macek B, Grond S, Link H, Nieselt K, Krismer B, Peschel A, Heilbronner S.
Horizontal transfer of bacteriocin biosynthesis genes requires metabolic adaptation to improve compound production and cellular fitnessMicrobiol Spectr. 2023 Feb 14;11(1):e0317622. doi: 10.1128/spectrum.03176-22. Epub 2022 Dec 6. PMID: 36472430; PMCID: PMC9927498.

Rohmer C, Dobritz R, Tuncbilek‐Dere D, Lehmann E, Gerlach D, George SE, Bae T, Nieselt K, Wolz C.
Influence of Staphylococcus aureus Strain Background on Sa3int Phage Life Cycle Switches
Viruses 2022, 14:2471 (doi.org/10.3390/v14112471)

Witte Paz, M, Harbig, T, Nieselt K.
Evidente – A visual analytics tool for data enrichment in SNP-based phylogenetic trees
Bioinformatics Advances 2022, 2(1):1-7, 2022, vbac075 (doi.org/10.1093/bioadv/vbac075)

Klein K, Marai GE, Nieselt KK, Zupan B.
Visualization of Biological Data-From Analysis to Communication (Dagstuhl Seminar 21401)
Dagstuhl Reports 2022, 11:9 (Schloss Dagstuhl-Leibniz-Zentrum für Informatik)

Mungan M, Harbig T, Perez NH, Edenhart  S, Stegmann Evi, Nieselt K, Ziemert N.
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria
Nucleic Acids Research Web Server 2022, gkac371 (doi.org/10.1093/nar/gkac371)

Hauser JN, Tchoupa AK, Zabel, Nieselt K, Ernst CM, Slavetinsky CJ, Peschel A.
Prokaryotic phospholipid translocation by ubiquitous PplT domain proteins
BioRχiv (doi.org/10.1101/2022.03.11.483950)

Pla-Díaz M, Sánchez-Busó L, Giacani L, Šmajs D, Bosshard PP, Bagheri HC, Schuenemann VJ, Nieselt K, Arora N, González-Candelas F.
Evolutionary processes in the emergence and recent spread of the syphilis agent, Treponema pallidum
Molecular Biology and Evolution 2022, 39:1 (doi.org/10.1093/molbev/msab318)

Kozlíková B, Krone M, Nieselt K, Raidou RG, Smit NN.
Foreword: Special section on the Eurographics Workshop on Visual Computing for Biology and Medicine (EG VCBM) 2020
Computers & Graphics, 2021 (doi.org/10.1016/j.cag.2021.08.004)

Neukamm J, Peltzer A, Nieselt K.
DamageProfiler: Fast damage pattern calculation for ancient DNA
Bioinformatics 2021, 37(20):3652–3653 (doi.org/10.1093/bioinformatics/btab190)

Harbig TA, Fratte J, Krone M, Nieselt K.
OmicsTIDE: Interactive Exploration of Trends in Multi-Omics Data
bioRχiv, 02 February 2021 (doi.org/10.1101/2021.02.01.428836)

Luqman A, Zabel S, Rahmdel S, Merz B, Gruenheit N, Harter J, Nieselt K, Götz F.
The Neuromodulator-Encoding sadA Gene Is Widely Distributed in the Human Skin Microbiome
Front. Microbiol., 01 December 2020 (https://doi.org/10.3389/fmicb.2020.573679)

Sulheim S, Kumelj T, van Dissel D, Salehzadeh-Yazdi A, Du C, van Wezel GP, Nieselt K, Almaas E, Wentzel A, Kerkhoven EJ.
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production
iScience 2020, 23:9 (doi.org/10.1016/j.isci.2020.101525)

Raue S, Fan SH, Rosenstein R, Zabel S, Luqman A, Nieselt K, Götz F.
The Genome of Staphylococcus epidermidis O47
Frontiers in Microbiology 2020, 11:2061 (doi: 10.3389/fmicb.2020.02061)

Neukamm J, Pfrengle S, Molak M, Seitz A, Francken, M, Eppenberger P, Avanzi C, Reiter E, Urban C. Welte B, Stockhammer PW, Teßmann B, Herbig A, Harvati K, Nieselt K, Krause J, Schuenmann VJ.
2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals
BMC Biology 2020, 18:108 (doi.org/10.1186/s12915-020-00839-8)

Odumosu BT, Augusta UN, Cano-Prieto C, Buchmann A, Nieselt K, Gross H.
Draft Genome Sequence of Ochrobactrum sp. Strain MC-1LL, a Bacterial Strain with Antimicrobial Properties, Isolated from Marine Sediments in Nigeria
Microbiology Resource Announcements 2020, 9(22):e00425-20 (doi: 10.1128/MRA.00425-20)

Luqman A, Muttaqin MZ, Yulaipi S, Ebner P, Matsuo M,  Zabel S, Tribelli PM, Nieselt K, Hidayati D, Götz F.
Trace amines produced by skin bacteria accelerate wound healing in mice
Communications Biology 2020, 3:277 (doi: 10.1038/s42003-020-1000-7)

Grimm F, Edl F, Kerscher SR, Nieselt K, Gugel I, Schuhmann MU.
Semantic segmentation of cerebrospinal fluid and brain volume with a convolutional neural network in pediatric hydrocephalus—transfer learning from existing algorithms
Acta Neurochirurgica 2020 (https://doi.org/10.1007/s00701-020-04447-x)

Shore JA, Holland BR, Sumner JG, Nieselt K, Wills PR.
The Ancient Operational Code is Embedded in the Amino Acid Substitution Matrix and aaRS Phylogenies
Journal of Molecular Evolution 2020, 88:136–150

Miess H, Arlt P, Apel AK, Weber T, Nieselt K, Hanssen F, Czemmel S, Nahnsen S, Gross H.
The Draft Whole-Genome Sequence of the Antibiotic Producer Empedobacter haloabium ATCC 31962 Provides Indications for its Taxonomic Reclassification
Microbiology Resource Announcements (MRA) 2019, 8(45):e01120-19

Bufe T, Hennig A, Klumpp J, Weiss A, Nieselt K, Schmidt H.
Differential transcriptome analysis of enterohemorrhagic Escherichia coli strains reveals differences in response to plant-derived compounds
BMC Microbiology 2019, 19:212 (https://doi.org/10.1186/s12866-019-1578-4)

Fan SH, Ebner P, Reichert S, Hertlein T, Zabel S, Lankapalli A, Nieselt K, Ohlsen K, Götz F.
MpsAB is important for Staphylococcus aureus virulence and growth at atmospheric CO2 levels
Nature Communications 2019, 10: 3627 (doi:10.1038/s41467-019-11547-5)

Hennig A, Nieselt K.
Efficient merging of genome profile alignments
Bioinformatics 2019, 35(14):i71-i80 (doi.org/10.1093/bioinformatics/btz377)

Denyer T, Ma XL, Klesen S, Scacchi E, Nieselt K, Timmermans MCP.
Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing
Developmental Cell 2019, 48(6):840-852 (doi.org/10.1016/j.devcel.2019.02.022)

Söllner JF, Leparc G, Zwick M, Schönberger T, Hildebrandt T, Nieselt K, Simon E.
Exploiting orthology and de novo transcriptome assembly to refine target sequence information
BMC Medical Genomics 2019, 12:69 (doi.org/10.1186/s12920-019-0524-5)

Schön ME, Nieselt K, Garnica S.
Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient
PLoS ONE 2018, 13(12):e0208493 (doi.org/10.1371/journal.pone.0208493)

Grillová L, Bawa T, Mikalová L, Gayet-Ageron A, Nieselt K, Strouhal M, Sednaoui P, Ferry T, Cavassini M, Lautenschlager S, Dutly F, Pla-Díaz M, Krützen M, González-Candelas F, Bagheri HC, Šmajs D, Arora N, Bosshard PP.
Molecular characterization of Treponema pallidum subsp. pallidum in Switzerland and France with a new multilocus sequence typing scheme
PLoS One 2018, 13(7):e0200773 (doi: 10.1371/journal.pone.0200773)

Knauf S, Gogarten J, Schuenemann V, De Nys H, Düx A, Strouhal M, Mikalová 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, Šmajs S, Nieselt K, Krause J, Calvignac-Spencer S.
Nonhuman primates across sub-Saharan Africa are infected with the yaws bacterium Treponema pallidum subsp. pertenue
Emerging Microbes & Infections 2018, 7(157) (doi: https://doi.org/10.1038/s41426-018-0156-4)

Müller A, Hennig A, Lorscheid S, Grondona P, Schulze-Osthoff K, Hailfinger S, Kramer D.
IκBζ is a key transcriptional regulator of IL-36–driven psoriasis-related gene expression in keratinocytes
PNAS 2018, 115 (40) 10088-10093 (doi: https://doi.org/10.1073/pnas.1801377115)

Seitz A, Hanssen F, Nieselt K.
DACCOR–Detection, characterization, and reconstruction of repetitive regions in bacterial genomes
PeerJ 2018, 6:e4742: (doi: https://doi.org/10.7717/peerj.4742)

Schuenemann VJ, Avanzi C, Krause-Kyora B, Seitz A, Herbig A, Inskip S, Bonazzi M, Reiter E, Urban C, Pedersen DD, Taylor GM, Singh P, Stewart GR, Velemínský P, Likovsky J, Marcsik A, Molnár E, Pálfi G, Mariotti V, Riga A, Belcastro MG, Boldsen JL, Nebel A, Mays S, Donoghue HD, Zakrzewski S, Benjak A, Nieselt K, Cole ST, Krause J.
Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe
PLOS Pathogens 2018, 14(5): e1006997. https://doi.org/10.1371/journal.ppat.1006997

Peltzer A, Mittnik A, Wang CC, Posth C, Begg T, Nieselt K, Krause J.
Inferring genetic origins and phenotypic traits of George Bähr, the architect of the Dresden Frauenkirche
Scientific Reports 2018, 8(1):2115 (doi: https://dx.doi.org/10.1038/s41598-018-20180-z)

Strouhal M, Oppelt J, Mikalová L, Arora N, Nieselt K, González-Candelas F, Šmajs D.
Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes.
BMC Research Notes 2018, 11(1):16 (doi: https://doi.org/10.1186/s13104-017-3106-7)

Fuchs S, Mehlan H, Bernhardt J, Hennig A, Michalik S, Surmann K, Pané-Farré J, Giese A, Weiss S, Backert L, Herbig A, Nieselt K, Hecker M, Völker U, Mäder U.
AureoWiki ̵ The repository of the Staphylococcus aureus research and annotation community.
International Journal of Medical Microbiology 2018, 308(6):558-568 (doi: 10.1016/j.ijmm.2017.11.011)

Söllner J, Leparc G, Hildebrandt T, Klein H, Thomas L, Stupka E, Simon E.
An RNA-Seq atlas of gene expression in mouse and rat normal tissues
Scientific Data 2017, 4, Article number: 170185 (doi:10.1038/sdata.2017.185)

Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K, Hajdinjak M, Salie T, Rohland N, Mallick S, Peltzer A, Heinze A, Olalde I, Ferry M, Harney E, Michel M, Stewardson K, Cerezo-Roman J, Chiumia C, Crowther A, Gomani-Chinedbvu E, Gidna AO, Grillo KM, Helenius IT, Hellenthal G, Helm R, Horton M, Lopez S, Mabulla AZP, Parkington J, Shipton C, Thomas MG, Tibesasa R, Welling M, Hayes VM, Kennett DJ, Ramesar R, Meyer M, Pääbo S, Patterson N, Morris AG, Boivin N, Pinhasi R, Krause J, Reich D.
Reconstructing Prehistoric African Population Structure
Cell 2017, 171(1):59-71 (doi: 10.1016/j.cell.2017.08.049)

Lazaridis I, Mittnik A, Patterson N, Mallick S, Rohland N, Pfrengle S, Furtwängler A, Peltzer A, Posth C, Vasilakis A, McGeorge PJP, Konsolaki-Yannopoulou E, Korres G, Martlew H, Michalodimitrakis M, Özsait M, Özsait N, Papathanasiou A, Richards M, Roodenberg SA, Tzedakis Y, Arnott R, Fernandes DM, Hughey JR, Lotakis DM, Navas PA, Maniatis Y, Stamatoyannopoulos JA, Stewardson K, Stockhammer P, Pinhasi R, Reich D, Krause J, and Stammatoyannopoulos G.
Genetic origins of the Minoans and Mycenaeans
Nature 2017, 548:214-218 (doi: 10.1038/nature23310).

Bauer J, Fillinger F, Förstner K, Herbig A, Jones A, Flinspach K, Sharma C, Gross H, Nieselt K, Apel K.
dRNA-seq Transcriptional Profiling of the FK506 Biosynthetic Gene Cluster in Streptomyces tsukubaensis NRRL18488 and General Analysis of the Transcriptome
RNA Biology 2017, 14(11:1617-1626 (doi:10.1080/15476286.2017.1341020)

Schuenemann VJ*, Peltzer A*, Welte B, van Pelt WP, Molak M, Wang CC, Furtwängler A, Urban C, Reiter E, Nieselt K, Teßmann B, Francken M, Harvati K, Haak W, Schiffels S, Krause J.
Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods
Nature Communications 2017, 8:15694 (doi: 10.1038/ncomms15694)

Seitz A, Nieselt K.
Improving ancient DNA genome assembly
PeerJ 2017, 5: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, 5(11) (doi: 10.1186/s40168-017-0233-2)

Hart ML, Rusch E, Kaupp M, Nieselt 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, 13(2):258-266 (https://doi.org/10.1007/s12015-016-9710-4)

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 2016, 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, 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 (doi.org/10.1016/j.ymeth.2015.06.012)

Hennig A, Bernhard J, Nieselt K.
Pan-Tetris – an interactive visualization for Pan-genomes
BMC Bioinformatics 2015, 16 (Suppl 11):S3 (doi: https://doi.org/10.1186/1471-2105-16-S11-S3)

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, 547495 (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 (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 2013, 19-20 (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(3):202-213 (doi: 10.1159/000100376)

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, 12(2):116-118 (doi: https://doi.org/10.1038/sj.mp.4001905)

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, 2006

Dietzsch J, Gehlenborg N, Nieselt K.
Mayday – a Microarray Data Analysis Workbench
Bioinformatics 2006, 22(8):1010-1012 (doi: https://doi.org/10.1093/bioinformatics/btl070). 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 2006, 66(10):5278-5286 (doi: 10.1158/0008-5472.CAN-05-4610)

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 2006, 1(1):9 (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 2005, 23:287-294

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

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 (https://doi.org/10.1057/palgrave.ivs.9500094)

Henz S, Huson D, Auch A, Nieselt-Struwe K, Schuster S.
Whole-genome prokaryotic phylogeny
Bioinformatics 2005, 21(10):2329-2335 (doi: 10.1093/bioinformatics/bth324)

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 2004, 14:455-460 (doi: 10.1101/gr.2538704)

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 Interspecific Variation of Primate gene Expression Patterns
Science 2002, 296:340-343 (doi 10.1126/science.1068996)

Nieselt-Struwe K, von Haeseler A.
Quartet-mapping, a generalization of the likelihood-mapping procedure
Molecular Biology and Evolution 2001, 18:1204-1219 (doi: 10.1093/oxfordjournals.molbev.a003907)

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 (doi: 10.1002/(SICI)1097-0177(200005)218:1<160::AID-DVDY14>3.0.CO;2-2)

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 (doi: https://doi.org/10.1016/S0301-4622(97)00064-1)

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 (doi: 10.1006/jtbi.1997.0404)

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(1):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(9):1619-1629 (doi: 10.1089/aid.1992.8.1619)

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

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.

2016

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

2014

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

2009

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