Peer reviewed publications from and with GenXPro

Health and Pharma

Weinelt N, Wächtershäuser KN, Celik G, Jeiler B, Gollin I, Zein L, Smith S, Andrieux G, Das T, Roedig J, Feist L, Rotter B, Boerries M, Pampaloni F, van Wijk SJL. LUBAC-mediated M1 Ub regulates necroptosis by segregating the cellular distribution of active MLKL. Cell Death Dis. 2024 Jan 20

Porkoláb G, Mészáros M, Szecskó A, Vigh JP, Walter FR, Figueiredo R, Kálomista I, Hoyk Z, Vizsnyiczai G, Gróf I, Jan JS, Gosselet F, Pirity MK, Vastag M, Hudson N, Campbell M, Veszelka S, Deli MA. Synergistic induction of blood-brain barrier properties. Proc Natl Acad Sci U S A. 2024 May 21;121(21):e2316006121. doi: 10.1073/pnas.2316006121. Epub 2024 May 15.

Ten Cate V, Rapp S, Schulz A, Pallares Robles A, Jurk K, KoeckT, Espinola-Klein C, Halank M, Seyfarth HJ, Beutel ME, Schuster AK, Marini F, Hobohm L, Lankeit M, Lackner KJ, Ruf W, Münzel T, Andrade-Navarro MA, Prochaska JH, Konstantinides SV, Wild PS.Circulating microRNAs predict recurrence and death following venous thromboembolism. J Thromb Haemost. 2023;Oct;21(10):2797-2810.

Koll FJ, Döring C, Olah C, Szarvas T, Köllermann J, Hoeh B, Chun FK, Reis H, Wild PJ. Optimizing identification of consensus molecular subtypes in muscle-invasive bladder cancer: a comparison of two sequencing methods and gene sets using FFPE specimens. BMC Cancer. 2023 Jun 4;23

Nold SP, Sych K, Imre G, Fuhrmann DC, Pfeilschifter J, Vutukuri R, Schnutgen F, Wittig I, Meisterknecht J, Frank S, Goren I. Reciprocal abrogation of PKM isoforms: contradictory outcomes and differing impact of splicing signal on CRISPR/Cas9 mediates gene editing in keratinocytes. FEBS J. 2023 May;290(9):2338-2365.

Majed SO, Mustafa SA. The profiles of miR-4510 expression level in breast cancer. Sci Rep. 2023 Feb 8;13(1):2262.

Wolf J, Kammrath Betancor P, Maier P, Heinzelmann SU, Jiang J, Lange C, Reinhard T, Schlunck G, Lapp T. Transcriptional Profiling Provides New Insights into Organ Culture-Induced Changes in Human Donor Corneas. Int J Mol Sci. 2022 Nov 22;23(23):14507

Chiocchetti AG, Yousaf A, Waltes R, Bernhard A, Martinelli A, Ackermann K, Haslinger D, Rotter B, Krezdorn N, Konrad K, Kohls G, Vetro A, Hervas A, Fernández-Rivas A, Freitag CM. The methylome in females with adolescent Conduct Disorder: Neural pathomechanisms and environmental risk factors. PLoS One. 2022 Jan 28;17(1):e0261691.

Bräuninger H, Stoffers B, Fitzek ADE, Meißner K, Aleshcheva G, Schweizer M, Weimann J, Rotter B, Warnke S, Edler C, Braun F, Roedl K, Scherschel K, Escher F, Kluge S, Huber TB, Ondruschka B, Schultheiss HP, Kirchhof P, Blankenberg S, Püschel K, Westermann D, Lindner D. Cardiac SARS-CoV-2 infection is associated with pro-inflammatory transcriptomic alterations within the heart. Cardiovasc Res. 2021 Oct 14

Kundu A, Kowarz E, Marschalek R. The role of reciprocal fusions in MLL-r acute leukemia: studying the chromosomal translocation t(6;11). Oncogene. 2021Oct;40(40):5902-5912.

Majed SO, Mustafa SA. MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker. BMC Cancer. 2021 Apr 29;21(1)

Guérit S, Fidan E, Macas J, Czupalla CJ, Figueiredo R, Vijikumar A, Yalcin BH, Thom S, Winter P, Gerhardt H, Devraj K, Liebner S. Astrocyte-derived Wnt growth factors are required for endothelial blood-brain barrier maintenance. Prog Neurobiol. 2021

Schwich OD, Blümel N, Keller M, Wegener M, Setty ST, Brunstein ME, Poser I, Mozos IRL, Suess B, Münch C, McNicoll F, Zarnack K, Müller-McNicoll M. SRSF3 and SRSF7 modulate 3’UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels. Genome Biol. 2021 Mar 11

Santa-Maria AR, Walter FR, Figueiredo R, Kincses A, Vigh JP, Heymans M, Culot M, Winter P, Gosselet F, Dér A, Deli MA. J Flow induces barrier and glycocalyx-related genes and negative surface charge in a lab-on-a-chip human blood-brain barrier modelCereb Blood Flow Metab. 2021

FebMahmood S, Sima R, Urbanova V, Trentelman JJA, Krezdorn N, Winter P, Kopacek P, Hovius JW, HajdusekIdentification of Tick Ixodes ricinus Midgut Genes Differentially Expressed During the Transmission of Borrelia afzelii Spirochetes Using a Transcriptomic Approach. O. Front Immunol. 2021 Feb 4;11:612412.

Guérit S, Fidan E, Macas J, Czupalla CJ, Figueiredo R, Vijikumar A, Yalcin BH, Thom S, Winter P, Gerhardt H, Devraj K, Liebner S.Astrocyte-derived Wnt growth factors are required for endothelial blood-brain barrier maintenance. Prog Neurobiol. 2021 Apr;199:101937.

Wiatr M, Staubach S, Figueiredo R, Stump-Guthier C, Ishikawa H, Schwerk C, Schroten H, Hanisch FG, Rudolph H, Tenenbaum T. Echovirus-30 Infection Alters Host Proteins in Lipid Rafts at the Cerebrospinal Fluid Barrier In Vitro.Microorganisms. 2020 Dec 10;8(12):1958.

Trentelman JJA, Sima R, Krezdorn N, Tomás-Cortázar J, Barriales D, Takumi K, Butler JM, Sprong H, Klouwens MJ, Urbanova V, Mahmood S, Winter P, Kopacek P, Anguita J, Hajdusek O, Hovius A combined transcriptomic approach to identify candidates for an anti-tick vaccine blocking B. afzelii transmission.JW. Sci Rep. 2020 Nov 18;10(1):20061

Wiatr M, Figueiredo R, Stump-Guthier C, Winter P, Ishikawa H, Adams O, Schwerk C, Schroten H, Rudolph H, Tenenbaum T. e.Polar Infection of Echovirus-30 Causes Differential Barrier Affection and Gene Regulation at the Blood-Cerebrospinal Fluid Barrier.Int J Mol Sci. 2020 Aug 29;21(17):6268. doi: 10.3390/ijms21176268. PMID: 32872518 Free PMC articl

Francisco DMF, Marchetti L, Rodríguez-Lorenzo S, Frías-Anaya E, Figueiredo RM; BtRAIN Network, Winter P, Romero IA, de Vries HE, Engelhardt B, Bruggmann R. Review. Advancing brain barriers RNA sequencing: guidelines from experimental design to publication.Fluids Barriers CNS. 2020 Aug 18;17(1):51. doi: 10.1186/s12987-020-00207-2. PMID: 32811511 Free PMC article.

Heymans M, Figueiredo R, Dehouck L, Francisco D, Sano Y, Shimizu F, Kanda T, Bruggmann R, Engelhardt B, Winter P, Gosselet F, Culot M. Contribution of brain pericytes in blood-brain barrier formation and maintenance: a transcriptomic study of cocultured human endothelial cells derived from hematopoietic stem cells. Fluids Barriers CNS. 2020 Jul 28;17(1):48. doi: 10.1186/s12987-020-00208-1. PMID: 32723387 Free PMC article.

Boneva 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.


Valadez-Moctezuma, E., Samah, S., Mascorro-Gallardo, J.O. et al. The first transcriptomic analyses of fruits and cladodes for comparison between three species of Opuntia. Genet Resour Crop Evol 70, 951–970 (2023).

Lebedeva MA, Dobychkina DA, Yashenkova YS, Romanyuk DA, Lutova LA. Local and systemic targets of the MtCLE35-SUNN pathway in the roots of Medicago truncatula. J Plant Physiol. 2023 Feb;281:153922.

Fondevilla S, Krezdorn N, Rubiales D, Rotter B, Winter P. Bulked segregant transcriptome analysis in pea identifies key expression markers for resistance to Peyronellaea pinodes. Sci Rep. 2022 Oct 28;12(1):18159.

Leitão, S.T., Santos, C., Araújo, S.d.S. et al. Shared and tailored common bean transcriptomic responses to combined fusarium wilt and water deficit. Hortic Res 8, 149 (2021).

Braun 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.

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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