Peer reviewed publications from and with GenXPro

Health and Pharma

Medicin_PharmaBoneva S, Schlecht A, Böhringer D, Mittelviefhaus H, Reinhard T, Agostini H, Auw-Haedrich C, Schlunck G, Wolf J, Lange C. 3′ MACE RNA-sequencing allows for transcriptome profiling in human tissue samples after long-term storage. Lab Invest. 2020 Oct;100(10):1345-1355.

Francisco, D.M.F., Marchetti, L., Rodríguez-Lorenzo, S. et al. Advancing brain barriers RNA sequencing: guidelines from experimental design to publication. Fluids Barriers CNS 17, 51 (2020).

Toptan T, Hoehl S, Westhaus S, Bojkova D, Berger A, Rotter B, Hoffmeier K,
Cinatl J Jr, Ciesek S, Widera M. Optimized qRT-PCR Approach for the Detection of
Intra- and Extra-Cellular SARS-CoV-2 RNAs. Int J Mol Sci. 2020 Jun

Lange C, Wolf J, Auw-Haedrich C, Schlecht A, Boneva S, Lapp T, Horres R, Agostini H, Martin G, Reinhard T, Schlunck G. Expression of the COVID-19 receptor ACE2 in the human conjunctiva. J Med Virol. 2020 May 6:10.1002/jmv.25981. d

Lipps C, Northe P, Figueiredo R, Rohde M, Brahmer A, Krämer-Albers EM, Liebetrau C, Wiedenroth CB, Mayer E, Kriechbaum SD, Dörr O, Nef H, Hamm CW, Keller T, Troidl C.Non-Invasive Approach for Evaluation of Pulmonary Hypertension Using Extracellular Vesicle-Associated Small Non-Coding RNA. Biomolecules. 2019 Oct 29;9(11):666.

Lange CAK, Lehnert P, Boneva SK, Zhang P, Ludwig F, Boeker M, Hoffmeier K, Horres R, Schlunck G, Reinhard T, Böhringer D, Auw-Haedrich C.I Increased expression of hypoxia-inducible factor-1 alpha and its impact on transcriptional changes and prognosis in malignant tumours of the ocular adnexa. Eye (Lond). 2018 Jul 31.

Tushev G, Glock C, Heumüller M, Biever A, Jovanovic M, Schuman EM.Alternative 3′ UTRs Modify the Localization, Regulatory Potential, Stability, and Plasticity of mRNAs in Neuronal Compartments.Neuron. 2018 May 2;98(3):495-511

Rezende F, Moll F, Walter M, Helfinger V, Hahner F, Janetzko P, Ringel C, Weigert A, Fleming I, Weissmann N, Kuenne C, Looso M, Rieger MA, Nawroth P, Fleming T, Brandes RP, Schröder K.The NADPH organizers NoxO1 and p47phox are both mediators of diabetes-induced vascular dysfunction in mice.Redox Biol. 2018 May;15:12-21.

Keller S, Kneissl J, Grabher-Meier V, Heindl S, Hasenauer J, Maier D, Mattes J, Winter P, Luber B. Evaluation of epidermal growth factor receptor signaling effects in gastric cancer cell lines by detailed motility-focused phenotypic characterization linked with molecular analysis. BMC Cancer. 2017 Dec 13;17(1):845.

Wanet A, Caruso M, Domelevo Entfellner JB, Najar M, Fattaccioli A, Demazy C, Evraerts J, El-Kehdy H, Pourcher G, Sokal E, Arnould T, Tiffin N, Najimi M,Renard P. The Transcription Factor 7-Like 2-Peroxisome Proliferator-Activated Receptor Gamma Coactivator-1 Alpha Axis Connects Mitochondrial Biogenesis and Metabolic Shift with Stem Cell Commitment to Hepatic Differentiation. Stem Cells.
2017 Oct;35(10):2184-2197.

Feil G, Horres R, Schulte J, Mack AF, Petzoldt S, Arnold C, Meng C, Jost L, Boxleitner J, Kiessling-Wolf N, Serbest E, Helm D, Kuster B, Hartmann I, Korff T, Hahne H. Bacterial Cellulose Shifts Transcriptome and Proteome of Cultured Endothelial Cells Towards Native Differentiation. Mol Cell Proteomics. 2017 Sep;16(9):1563-1577..

Agarwal R, Cao Y, Hoffmeier K, Krezdorn N, Jost L, Meisel AR, Jüngling R, Dituri F, Mancarella S, Rotter B, Winter P, Giannelli G.Precision medicine for hepatocelluar carcinoma using molecular pattern diagnostics: results from a preclinical pilot study. Cell Death Dis. 2017 Jun 8;8(6):e2867.

Casado-Díaz A, Anter J, Müller S, Winter P, Quesada-Gómez JM, Dorado G.Transcriptomic analyses of the anti-adipogenic effects of oleuropein in human mesenchymal stem cells. Food Funct. 2017 Mar 22;8(3):1254-1270

Cao Y, Agarwal R, Dituri F, Lupo L, Trerotoli P, Mancarella S, Winter P, Giannelli G. NGS-based transcriptome profiling reveals biomarkers for companion diagnostics of the TGF-β receptor blocker galunisertib in HCC. Cell Death Dis. 2017 Feb 23;8(2):e2634.

Zawada AM, Zhang L, Emrich IE, Rogacev KS, Krezdorn N, Rotter B, Fliser D, Devaux Y, Ziegler-Heitbrock L, Heine GH. MicroRNA profiling of human intermediate monocytes. Immunobiology. 2017 Mar;222(3):587-596.

Casado-Díaz A, Anter J, Müller S, Winter P, Quesada-Gómez JM, Dorado G. Transcriptomic Analyses of Adipocyte Differentiation From Human Mesenchymal Stromal-Cells (MSC). J Cell Physiol. 2016 Jun 28

Fell LH, Seiler-Mußler S, Sellier AB, Rotter B, Winter P, Sester M, Fliser D, Heine GH, Zawada AM.Impact of individual intravenous iron preparations on the differentiation of monocytes towards macrophages and dendritic cells. Nephrol Dial Transplant. 2016 Mar 24.

Giannelli G, Mikulits W, Dooley S, Fabregat I, Moustakas A, ten Dijke P, Portincasa P, Winter P, Janssen R, Leporatti S, Herrera B, Sanchez A. The rationale for targeting TGF-β in chronic liver diseases. Eur J Clin Invest. 2016 Apr;46(4):349-61.

Wecker T, Hoffmeier K, Plötner A, Grüning BA, Horres R, Backofen R, Reinhard T, Schlunck G.MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing.Invest Ophthalmol Vis Sci. 2016 Apr 1;57(4):1706-1713.

Zawada AM, Schneider JS, Michel AI, Rogacev KS, Hummel B, Krezdorn N, Müller S, Rotter B, Winter P, Obeid R, Geisel J, Fliser D, Heine GH.DNA methylation profiling reveals differences in the 3 human monocyte subsets and identifies uremia to induce DNA methylation changes during differentiation. Epigenetics. 2016 Apr 2;11(4):259-72

Mazzocca A, Dituri F, De Santis F, Filannino A, Lopane C, Betz RC, Li YY, Mukaida N, Winter P, Tortorella C, Giannelli G, Sabbà C. Lysophosphatidic Acid Receptor LPAR6 Supports the Tumorigenicity of Hepatocellular Carcinoma.Cancer Res. 2015 Feb 1;75(3):532-43. doi: 10.1158/0008-5472.CAN-14-1607.

Hofer TP, Zawada AM, Frankenberger M, Skokann K, Satzl AA, Gesierich W,
Schuberth M, Levin J, Danek A, Rotter B, Heine GH, Ziegler-Heitbrock L. slan-defined subsets of CD16-positive monocytes:Characterization of subsets of the CD16-positive monocytes: impact of granulomatous inflammation and M-CSF-receptor mutation. Blood. 2015 Oct 6. pii: blood-2015-06-651331.

Afonso-Grunz F, Hoffmeier K, Müller S, Westermann AJ, Rotter B, Vogel J, Winter P, Kahl G Dual 3’Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells. BMC Genomics. 2015 Apr 19;16:323.

Müller S, Raulefs S, Bruns P, Afonso-Grunz F, Plötner A, Thermann R, Jäger C, Schlitter AM, Kong B, Regel I, Roth WK, Rotter B, Hoffmeier K, Kahl G, Koch I, Theis FJ, Kleeff J, Winter P, Michalski CW. Next-generation sequencing reveals novel differentially regulated mRNAs, lncRNAs, miRNAs, sdRNAs and a piRNA in pancreatic cancer. Mol Cancer. 2015 Apr 25;14(1):94.

Nold-Petry CA, Lo CY, Rudloff I, Elgass KD, Li S, Gantier MP, Lotz-Havla AS, Gersting SW, Cho SX, Lao JC, Ellisdon AM, Rotter B, Azam T, Mangan NE, Rossello FJ, Whisstock JC, Bufler P, Garlanda C, Mantovani A, Dinarello CA, Nold MF. IL-37 requires the receptors IL-18Ra and IL-1R8 (SIGIRR) to carry out its multifaceted anti-inflammatory program upon innate signal transduction.Nat Immunol. 2015 Mar 2

Müller S, Nowak K.Exploring the miRNA-mRNA regulatory network in clear cell renal cell carcinomas by next-generation sequencing expression profiles.Biomed Res Int. 2014;2014:948408

Zawada AM, Rogacev KS, Müller S, Rotter B, Winter P, Fliser D, Heine GH. Massive Analysis of cDNA Ends (MACE) and miRNA expression profiling identifies proatherogenic pathways in chronic kidney disease MACE and miRNA profiling in CKD.Epigenetics. 2013 Nov 1;9(1)

Zawada AM, Rogacev KS, Hummel B, Gr?n OS, Friedrich A, Rotter B, Winter P, Geisel J, Fliser D, Heine GH. SuperTAG Methylation-Specific Digital Karyotyping (SMSDK) Reveals Uremia Induced Epigenetic Dysregulation of Atherosclerosis-Related Genes Circ Cardiovasc Genet. 2012; CIRCGENETICS.112.963207


AgricultureBraun EM, Tsvetkova N, Rotter B, Siekmann D, Schwefel K, Krezdorn N, Plieske J, Winter P, Melz G, Voylokov AV, Hackauf B. Gene Expression Profiling and Fine Mapping Identifies a Gibberellin 2-Oxidase Gene Co-segregating With the Dominant Dwarfing Gene Ddw1 in Rye (Secale cereale L.). Front Plant Sci. 2019 Jul 3;10:857. doi: 10.3389/fpls.2019.00857.

Zhernakov AI, Shtark OY, Kulaeva OA, Fedorina JV, Afonin AM, Kitaeva AB, Tsyganov VE, Afonso-Grunz F, Hoffmeier K, Rotter B, Winter P, Tikhonovich IA, Zhukov VA.Mapping-by-sequencing using NGS-based 3′-MACE-Seq reveals a new mutant allele of the essential nodulation gene Sym33 (IPD3) in pea (Pisum sativum L.). PeerJ. 2019 Apr 2;7:e6662. doi: 10.7717/peerj.6662. eCollection 2019.

Kirchner TW, Niehaus M, Rössig KL, Lauterbach T, Herde M, Küster H, Schenk MK.Molecular Background of Pi Deficiency-Induced Root Hair Growth in Brassica carinata – A Fasciclin-Like Arabinogalactan Protein Is Involved. Front Plant Sci.2018 Sep 19;9:1372.

Parreira JR, Balestrazzi A, Fevereiro P, Araújo SS.Maintaining Genome Integrity during Seed Development in Phaseolus vulgaris L.: Evidence from a Transcriptomic Profiling Study.Genes (Basel). 2018 Sep 20;9(10)

Santos C, Almeida NF, Alves ML, Horres R, Krezdorn N, Leitão ST, Thaïs AF, Rotter B, Winter P, Rubiales D & Vaz Patto MC. First genetic linkage map of Lathyrus ciceraHorticulture Researchvolume 5, Article number: 45 (2018) based on RNA sequencing-derived markers: Key tool for genetic mapping of disease resistance Horticulture Researchvolume 5, Article number: 45 (2018)

Hradilová I, Trněný O, Válková M, Cechová M, Janská A, Prokešová L, Aamir K, Krezdorn N, Rotter B, Winter P, Varshney RK, Soukup A, Bednář P, Hanáček P, Smýkal P.A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea (Pisum sp.).Front Plant Sci. 2017 Apr 25;8:542

Weiß S, Bartsch M, Winkelmann T.Transcriptomic analysis of molecular responses in Malus domestica ‘M26’ roots affected by apple replant disease.Plant Mol Biol. 2017 Jun;94(3):303-318.

Zhernakov A, Rotter B, Winter P, Borisov A, Tikhonovich I, Zhukov V. Massive Analysis of cDNA Ends (MACE) for transcript-based marker design in pea (Pisum sativum L.). Genom Data. 2016 Dec 12;11:75-76.

Bojahr J, Nhengiwa O, Krezdorn N, Rotter B, Saal B, Ruge-Wehling B, Struck C, Winter P.Massive analysis of cDNA ends (MACE) reveals a co-segregating candidate gene for LpPg1 stem rust resistance in perennial ryegrass (Lolium perenne). Theor Appl Genet. 2016 Oct;129(10):1915-32.

Serfling A., Templer S.E., Winter P.,  and Ordon F. Microscopic and Molecular Characterization of the Prehaustorial Resistance against Wheat Leaf Rust (Puccinia triticina) in Einkorn (Triticum monococcum) Front. Plant Sci., 09 November 2016

Bromage TG,  Idaghdour Y, Lacruz RS, Crenshaw TD,  Ovsiy O, Rotter B,  Hoffmeier K, Schrenk F The Swine Plasma Metabolome Chronicles “Many Days” Biological Timing and Functions Linked to Growth PLOS ONE January 6, 2016

Fondevilla S, Krezdorn N, Rotter B, Kahl G, Winter P.In planta Identification of Putative Pathogenicity Factors from the Chickpea Pathogen Ascochyta rabiei by De novo Transcriptome Sequencing Using RNA-Seq and Massive Analysis of cDNA Ends. Front Microbiol. 2015 Dec 1;6:1329.

Fischer K, Dieterich R, Nelson MN, Kamphuis LG, Singh KB, Rotter B, Krezdorn N, Winter P, Wehling P, Ruge-Wehling B.Characterization and mapping of LanrBo: a locus conferring anthracnose resistance in narrow-leafed lupin (Lupinus angustifolius L.). Theor Appl Genet. 2015 Oct;128(10):2121-30.

Bokszczanin KL, Krezdorn N, Fragkostefanakis S, Müller S, Rycak L, Chen Y, Hoffmeier K, Kreutz J, Paupière MJ, Chaturvedi P, Iannacone R, Müller F, Bostan H, Chiusano ML, Scharf KD, Rotter B, Schleiff E, Winter P; SPOT-ITN Consortium (Solanaceae Pollen Thermotolerance Initial Training Network Consortium)SPOT-ITN Consortium (Solanaceae Pollen Thermotolerance Initial Training Network Consortium). Identification of novel small ncRNAs in pollen of tomato. BMC Genomics. 2015 Sep 18;16(1):714

Behringer D, Zimmermann H, Ziegenhagen B, Liepelt S (2015) Differential Gene Expression Reveals Candidate Genes for Drought Stress Response in Abies alba (Pinaceae). PLoS ONE 10(4): e0124564.

Simm S, Fragkostefanakis S, Paul P, Keller M, Einloft J, Scharf KD, Schleiff E.
Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum. Bioinform Biol Insights. 2015 Feb 4;9:1-17. doi: 10.4137/BBI.S20751.

Fragkostefanakis S, Simm S, Paul P, Bublak D, Scharf KD, Schleiff E. Chaperone network composition in Solanum lycopersicum explored by transcriptome profiling and microarray meta-analysis. Plant Cell Environ. 2015 Apr;38(4):693-709

Almeida NF, Krezdorn N, Rotter B, Winter P, Rubiales D, Vaz Patto MC. Lathyrus sativus transcriptome resistance response to Ascochyta lathyri investigated by deepSuperSAGE analysis. Front Plant Sci. 2015 Mar 20;6:178

Simm S, Fragkostefanakis S, Paul P, Keller M, Einloft J, Scharf KD, Schleiff E. Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum. Bioinform Biol Insights. 2015 Feb 4;9:1-17

Almeida NF, Leitão ST, Krezdorn N, Rotter B, Winter P, Rubiales D, Vaz Patto MC. Allelic diversity in the transcriptomes of contrasting rust-infected genotypes of Lathyrus sativus, a lasting resource for smart breeding. BMC Plant Biol. 2014 Dec 19;14:376.

Afonso-Grunz F, Molina C, Hoffmeier K, Rycak L, Kudapa H, Varshney RK, Drevon JJ, Winter P, Kahl G. Genome-based analysis of the transcriptome from mature chickpea root nodules. Front Plant Sci. 2014 Jul 11;5:325

Yakovlev IA, Lee Y, Rotter B, Jorunn EO , Skrøppa T, Johnsen Ø, Fossdal CG.
Temperature-dependent differential transcriptomes during formation of an epigenetic memory in Norway spruce embryogenesis Tree Genetics & Genomes; April 2014, Volume 10, Issue 2, pp 355-366

Draffehn AM, Li L, Krezdorn N, Ding J, Lübeck J, Strahwald J, Muktar MS, Birgit Walkemeier B, Rotter B and Gebhardt C .Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity. Front. Plant Sci. 2013 October

Yakovlev I, Lee YK, Rotter B, Skr?ppa T, Olsen JE, Johnsen ?, Fossda CG; Molecular dissection of an adaptive epigenetic memory mechanism in norway spruce BMC Proceedings 2011,5 (Suppl 7):O2

Yang ZB, Eticha D, Rotter B, Rao IM, Horst WJ. “Physiological and molecular analysis of polyethylene glycol-induced reduction of aluminium accumulation in the root tips of common bean (Phaseolus vulgaris)” New Phytol. 2011 Jun 13. doi: 10.1111/j.1469-8137.2011.03784.x.

Molina C. Zaman-Allah M, Khan F., Fatnassi N, Horres R, Rotter B. Steinhauer D. Amenc L, Drevon JJ, Winter P, and Kahl G “The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE” BMC Plant Biology 2011, 11:31doi:10.1186/1471-2229-11-31

Molina C. , Rotter B., Horres R., Udupa S.M.,Besser B., Bellarmino L., Baum M., Matsumura H.,Terauchi R., Kahl G., Winter P. SuperSAGE: the drought stress-responsive transcriptome of chickpea roots” BMC Genomics 2008, 9:553 doi:10.1186/1471-2164-9-553

Zawada AM, Rogacev KS, Rotter B, Winter P, Marell RR, Fliser D, Heine GH. SuperSAGE evidence for CD14++CD16+ monocytes as a third monocyte subset.
Blood. 2011 Jul 29

Non-models and methods


Lee BH, Garmyn D, Gal L, Guérin C, Guillier L, Rico A, Rotter B, Nicolas P,
Piveteau P. Exploring Listeria monocytogenes Transcriptomes in Correlation with
Divergence of Lineages and Virulence as Measured in Galleria mellonella. Appl
Environ Microbiol. 2019 Oct 16;85(21):e01370-19.

PMID: 31471303; PMCID: PMC6803300.Tosches MA, Yamawaki TM, Naumann RK, Jacobi AA, Tushev G, Laurent G. Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles. Science. 2018 May 25;360(6391):881-888.

Scheider J, Afonso-Grunz F, Jessl L, Hoffmeier K, Winter P, Oehlmann J.Morphological and transcriptomic effects of endocrine modulators on the gonadal differentiation of chicken embryos: The case of tributyltin (TBT).Toxicol Lett. 2018 Mar 1;284:143-151

Hoppeler F, Rotter B, Krezdorn N,  Pauls SU  (2016) A larval transcriptome of the limnephilid caddisfly Micropterna lateralis (Stephens, 1837)  Aquatic Insects, 37:3, 253-257
Afonso-Grunz F, Müller S. Principles of miRNA-mRNA interactions: beyond sequence complementarity. Cell Mol Life Sci. 2015 Aug;72(16):3127-41.

Zajac BK, Amendt J, Horres R, Verhoff MA, Zehner R. De novo transcriptome analysis and highly sensitive digital gene expression profiling of Calliphora vicina (Diptera: Calliphoridae) pupae using MACE (Massive Analysis of cDNA Ends). Forensic Sci Int Genet. 2015 Mar;15:137-46

Reister M, Hoffmeier K, Krezdorn N, Rotter B, Liang C, Rund S, Dandekar T, Sonnenborn U, Oelschlaeger TA. Complete genome sequence of the gram-negative probiotic Escherichia coli strain Nissle 1917. J Biotechnol. 2014 Oct 10;187:106-7.

Müller S, Rycak L, Afonso-Grunz F, Winter P, Zawada AM, Damrath E, Scheider J, Schmäh J, Koch I, Kahl G, Rotter B. APADB: a database for alternative polyadenylation and microRNA regulation events Database (Oxford). 2014 Jul 22;2014.

Philipp O, Hamann A, Servos J, Werner A, Koch I, Osiewacz HD. A Genome-Wide Longitudinal Transcriptome Analysis of the Aging Model Podospora anserina.
PLoS One. 2013 Dec 20;8(12):e83109. doi: 10.1371/journal.pone.0083109.

Müller S, Rycak L, Winter P, Kahl G, Koch I, Rotter B. omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data. Bioinformatics. 2013 Aug 23.

Rajeev K Varshney, Chi Song , Rachit K Saxena , Sarwar Azam, Sheng Yu, Andrew G Sharpe, Steven Cannon, Jongmin Baek, Benjamin D Rosen, Bunyamin Tar?an, Teresa Millan, Xudong Zhang, Larissa D Ramsay, Aiko Iwata, Ying Wang , William Nelson, Andrew D Farmer, Pooran M Gaur , Carol Soderlund ,R Varma Penmetsa , Chunyan Xu , Arvind K Bharti, Weiming He, Peter Winter et al. Draft genome sequence of chickpea (Cicer arietinum)provides a resource for trait improvement. Nature Biotechnology 31, 240?246(2013)doi:10.1038/nbt.2491

Lenz TL, Eizaguirre C, Rotter B, Kalbe M, Milinski M. Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis. Mol Ecol. 2013 Feb;22(3):774-86. doi: 10.1111/j.1365-294X.2012.05756.x. Epub 2012 Sep 13.

Kahl G, Molina C, Rotter B, J?ngling R, Frank A, Krezdorn N, Hoffmeier K, Winter P
Reduced representation sequencing of plant stress transcriptomes Journal of Plant Biochemistry and Biotechnology; October 2012, Volume 21, Issue 1 Supplement, pp 119-127

Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M. Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance.BMC Genomics 2011, 12:317

Gilardoni PA, Schuck S, J?ngling R, Rotter B, Baldwin IT, Bonaventure G.
“SuperSAGE analysis of the Nicotiana attenuata transcriptome after fatty acid-amino acid elicitation (FAC): identification of early mediators of insect responsesBMC Plant Biol. 2010 Apr 14;10:66

Sharbel TF, Voigt ML, Corral JM, Galla G, Kumlehn J, Klukas C, Schreiber F, Vogel H, Rotter B “Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns” Plant Cell. 2010 Mar;22(3):655-71. Epub 2010 Mar 19

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