Scientific Publications


ecSeq actively takes part in current biomedical research with regular publications in high-impact journals. The peer-reviewed publications listed below are from our company, our team members, or from joint projects with customers, or collaborators. Full documents in electronic form may be directly downloaded at the journals website linked to every entry.



  • Hackenberg M, Langenberger D, Schwarz A, Erhart J, Kotsyfakis M: 'In-silico target network analysis of de novo-discovered, tick saliva-specific microRNAs reveals important combinatorial effects in their interference with vertebrate host physiology', RNA. rna.061168.117 (2017)

  • Bernhart SH, Kretzmer H, Holdt LM, Jühling F, Ammerpohl O, Bergmann AK, Northoff BH, Doose G, Siebert R, Stadler PF, Hoffmann S: 'Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer'. Nature Science Report, 6:37393 (2016)

  • Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VA, Collatz M, Doose G, Eggenhofer F, Ewald J, Fallmann J, Feldhahn LM, Fricke M, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Kanton S, Linde J, Mostajo N, Ochsenreiter R, Riege K, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M: 'Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells'. Nature Science Report, 6:34589 (2016)

  • Shostak A, Ruppert B, Ha N, Bruns P, Toprak UH; ICGC MMML-Seq Project, Eils R, Schlesner M, Diernfellner A, Brunner M: 'MYC/MIZ1-dependent gene repression inversely coordinates the circadian clock with cell cycle and proliferation'. Nature Communications, 7:11807 (2016)

  • Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH: 'The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons'. Nature Genetics,48(4):427-437 (2016)

  • Esperanza M, Seoane M, Rioboo C, Herrero C, Cid A: 'Early alterations on photosynthesis-related parameters in Chlamydomonas reinhardtii cells exposed to atrazine: A multiple approach study', Science of The Total Environment, 554:237-245 (2016)

  • Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Hummel M, Karsch D, Kerstens HH, Klapper W, Kreuz M, Lawerenz C, Lenze D, Loeffler M, López C, MacLeod RA, Martens JH, Kulis M, Martín-Subero JI, Möller P, Nagel I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG; ICGC MMML-Seq project.; BLUEPRINT project., Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B.: 'DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control'. Nature Genetics, 47(11):1316-25. (2016)

  • Jühling F, Kretzmer H, Bernhart SH, Otto C, Stadler PF, Hoffmann S: 'metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data', Genome Res. 26(2):256-62.. (2015)

  • Doose G, Haake A, Bernhart SH, López C, Duggimpudi S, Wojciech F, Bergmann AK, Borkhardt A, Burkhardt B, Claviez A, Dimitrova L, Haas S, Hoell JI, Hummel M, Karsch D, Klapper W, Kleo K, Kretzmer H, Kreuz M, Küppers R, Lawerenz C, Lenze D, Loeffler M, Mantovani-Löffler L, Möller P, Ott G, Richter J, Rohde M, Rosenstiel P, Rosenwald A, Schilhabel M, Schneider M, Scholz I, Stilgenbauer S, Stunnenberg HG, Szczepanowski M, Trümper L, Weniger MA; ICGC MMML-Seq Consortium, Hoffmann S, Siebert R, Iaccarino I: 'MINCR is a MYC-induced lncRNA able to modulate MYCs transcriptional network in Burkitt lymphoma cells'. PNAS, 112(38):E5261-70. (2015)

  • Wagener R, Aukema SM, Schlesner M, Haake A, Burkhardt B, Claviez A, Drexler HG, Hummel M, Kreuz M, Loeffler M, Rosolowski M, López C, Möller P, Richter J, Rohde M, Betts MJ, Russell RB, Bernhart SH, Hoffmann S, Rosenstiel P, Schilhabel M, Szczepanowski M, Trümper L, Klapper W, Siebert R; ICGC MMML-Seq-Project; "Molecular Mechanisms in Malignant Lymphomas" Network Project of the Deutsche Krebshilfe: 'The PCBP1 gene encoding poly(rC) binding protein I is recurrently mutated in Burkitt lymphoma', Genes Chromosomes Cancer, 54(9):555-64 (2015)

  • Esperanza M, Seoane M, Rioboo C, Herrero C, Cid A: 'Chlamydomonas reinhardtii cells adjust the metabolism to maintain viability in response to atrazine stress', Aquatic Toxicology, 165:64-72 (2015)

  • Gardner PP, Fasold M, Burge SW, Ninova M, Hertel J, Kehr S, Steeves TE, Griffiths-Jones S, Stadler PF: 'Conservation and Losses of Non-Coding RNAs in Avian Genomes', PLoS One, 10(3):e0121797 (2015)

  • Nitsche A, Rose D, Fasold M, Reiche K, Stadler PF: 'Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved', RNA, [Epub ahead of print] (2015)

  • Sygnecka K, Heine C, Scherf N, Fasold M, Binder H, Scheller C, Franke H: 'Nimodipine enhances neurite outgrowth in dopaminergic brain slice co-cultures', Int J Dev Neurosci., 40:1-11 (2015)

  • Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF: 'Atypical RNAs in the coelacanth transcriptome', J Exp Zool B Mol Dev Evol., 322(6):342-51 (2014)

  • Otto C, Stadler PF, Hoffmann S: 'Lacking alignments? The next-generation sequencing mapper segemehl revisited', Bioinformatics. 30(13):1837-43.. (2014)

  • Hackermüller J, Reiche K, Otto C, Hösler N, Blumert C, Brocke-Heidrich K, Böhlig L, Nitsche A, Kasack K, Ahnert P, Krupp W, Engeland K, Stadler PF, Horn F: 'Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs', Genome Biol. 15(3):R48.. (2014)

  • Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF: 'plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants', Front Plant Sci., 5:708. (2014)

  • Sarah A. Munro, Steven P. Lund, P. Scott Pine, Hans Binder, Djork-Arné Clevert, Ana Conesa, Joaquin Dopazo, Mario Fasold, Sepp Hochreiter, Huixiao Hong, Nadereh Jafari, David P. Kreil, Paweł P. Łabaj, Sheng Li, Yang Liao, Simon M. Lin, Joseph Meehan, Christopher E. Mason, Javier Santoyo-Lopez, Robert A. Setterquist, Leming Shi, Wei Shi, Gordon K. Smyth, Nancy Stralis-Pavese, Zhenqiang Su, Weida Tong, Charles Wang, Jian Wang, Joshua Xu, Zhan Ye, Yong Yang, Ying Yu & Marc Salit: 'Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures', Nature Communications, 5:5125. (2014)

  • Rivarola-Duarte L, Otto C, Jühling F, Schreiber S, Bedulina D, Jakob L, Gurkov A, Axenov-Gribanov D, Sahyoun AH, Lucassen M, Hackermüller J, Hoffmann S, Sartoris F, Pörtner HO, Timofeyev M, Luckenbach T, Stadler PF: 'A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus', J Exp Zool B Mol Dev Evol. 322(3):177-89.. (2014)

  • Su Z, Labaj PP, Li S, Thierry-Mieg J, Thierry-Mieg D, Shi W, Wang C, Schroth GP, Setterquist RA, Thompson JF, Jones WD, Xiao W, Xu W, Jensen RV, Kelly R, Xu J, Conesa A, Furlanello C, Gao H, Hong H, Jafari N, Letovsky S, Liao Y, Lu F, Oakeley EJ, Peng Z, Praul CA, Santoyo-Lopez J, Scherer A, Shi T, Smyth GK, Staedtler F, Sykacek P, Tan XX, Thompson EA, Vandesompele J, Wang MD, Wang J, Wolfinger RD, Zavadil J, Auerbach SS, Bao W, Binder H, Blomquist T, Brilliant MH, Bushel PR, Cai W, Catalano JG, Chang CW, Chen T, Chen G, Chen R, Chierici M, Chu TM, Clevert DA, Deng Y, Derti A, Devanarayan V, Dong Z, Dopazo J, Du T, Fang H, Fang Y, Fasold M, Fernandez A, Fischer M, Furió-Tari P, Fuscoe JC, Caimet F, Gaj S, Gandara J, Gao H, Ge W, Gondo Y, Gong B, Gong M, Gong Z, Green B, Guo C, Guo L, Guo LW, Hadfield J, Hellemans J, Hochreiter S, Jia M, Jian M, Johnson CD, Kay S, Kleinjans J, Lababidi S, Levy S, Li QZ, Li L, Li L, Li P, Li Y, Li H, Li J, Li S, Lin SM, López FJ, Lu X, Luo H, Ma X, Meehan J, Megherbi DB, Mei N, Mu B, Ning B, Pandey A, Pérez-Florido J, Perkins RG, Peters R, Phan JH, Pirooznia M, Qian F, Qing T, Rainbow L, Rocca-Serra P, Sambourg L, Sansone SA, Schwartz S, Shah R, Shen J, Smith TM, Stegle O, Stralis-Pavese N, Stupka E, Suzuki Y, Szkotnicki LT, Tinning M, Tu B, van Delft J, Vela-Boza A, Venturini E, Walker SJ, Wan L, Wang W, Wang J, Wang J, Wieben ED, Willey JC, Wu PY, Xuan J, Yang Y, Ye Z, Yin Y, Yu Y, Yuan YC, Zhang J, Zhang KK, Zhang W, Zhang W, Zhang Y, Zhao C, Zheng Y, Zhou Y, Zumbo P, Tong W, Kreil DP, Mason CE, Shi L.: 'A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium', Nature Biotechnology, 32(9):903-914. (2014)

  • Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt L, Teupser D, Hackermüeller J, Stadler PF: 'A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection', Genome Biology, 15:R34, doi:10.1186/gb-2014-15-2-r34 (2014)

  • Hertel J, Langenberger D, Stadler PF: 'Computational prediction of microRNA genes', in J. Gorodkin, W.L. Ruzzo, (eds).: RNA Sequence, Structure and Function: Computational and Bioinformatic Methods. Volume 1097 of Methods in Molecular Biology, Humana Press, New York. (2014)

  • Hezaveh K, Bernhart S, Hoffmann S, Langenberger D, Schlesner M, Stadler PF, Binder V, Lenze D, Siebert R, Hummel M, Borkhardt A: 'In-Depth miRNA Profiling Of Germinal Center Derived B-Cell Lymphomas By Next Generation Sequencing: A Report From The German Icgc-Mmml-Seq Project', Blood 122 (21), 2500-2500. (2013)

  • Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SAJR, Behiati S, Biankin AV, Bignell GR, Bolli N, Borg A, Boerresen-Dale A, Boyault S, Burkhardt B, Butler AP, Caldas C, Davies HR, Desmedt C, Eils R, Eyfjord JE, Foekens JA, Greaves M, Hosoda F, Hutter B, Ilicic T, Imbeaud S, Imielinsk M, Jäger N, Jones DTS, Jones D, Knappskog S, Kool M, Lakhani SR, López-Otín C, Martin S, Munshi NC, Nakamura H, Northcott PA, Pajic M, Papaemmanuil E, Paradiso A, Pearson JV, Puente XS, Raine K, Ramakrishna M, Richardson AL, Richter J, Rosenstiel P, Schlesner M, Schumacher TN, Span PN, Teague JW, Totoki Y, Tutt ANJ, Valdés-Mas R, van Buuren MM, van 't Veer L, Vincent-Salomon A, Waddell N, Yates LR, Australian Pancreatic Cancer Gen Initiative, ICGC Breast Cancer Consortium, ICGC MMML-Seq Consortium, ICGC PedBrain, Zucman-Rossi J, Futreal PA, McDermott U, Lichter P, Meyerson M, Grimmond SM, Siebert R, Campo E, Shibata T, Pfister SM, Campbell PJ, Stratton MR: 'Signatures of mutational processes in human cancer'', Nature, 500(7463):415-21. (2013)

  • Holdt LM, Hoffmann S, Sass K, Langenberger D, Scholz M, Krohn K, Finstermeier K, Stahringer A, Wilfert W, Beutner F, Gielen S, Schuler G, Gäbel G, Bergert H, Bechmann I, Stadler PF, Thiery J, Teupser D: 'Alu Elements in ANRIL Non-Coding RNA at Chromosome 9p21 Modulate Atherogenic Cell Functions through Trans-Regulation of Gene Networks', PLoS Genetics, 9(7): e1003588. (2013)

  • Doose G, Alexis M, Kirsch R, Findeiß S, Langenberger D, Machne R, Mörl M, Hoffmann S, Stadler PF: 'Mapping the RNA-Seq trash bin: Unusual transcripts in prokaryotic transcriptome sequencing data', RNA Biology. (2013)

  • Fasold M, Binder H: 'AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data', Bioinformatics., 29(1):129-31 (2013)

  • Hertel J, Bartschat S, Wintsche A, Otto C; Students of the Bioinformatics Computer Lab., Stadler PF: 'Evolution of the let-7 microRNA family', RNA Biol. 9(3):231-41.. (2012)

  • Otto C, Stadler PF, Hoffmann S: 'Fast and sensitive mapping of bisulfite-treated sequencing data', Bioinformatics. 28(13):1698-704.. (2012)

  • Otto C, Reiche K, Hackermüller J: 'Detection of differentially expressed segments in tiling array data', Bioinformatics. 28(11):1471-9.. (2012)

  • Doose G, Metzler D: 'Bayesian sampling of evolutionarily conserved RNA secondary structures with pseudoknots', Bioinformatics, 28(17):2242-8.. (2012)

  • Smialowski P, Doose G, Torkler P, Kaufmann S, Frishman D: 'PROSO II--a new method for protein solubility prediction', FEBS J., 279(12):2192-200.. (2012)

  • Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B, Rosolowski M, Ammerpohl O, Wagener R, Bernhart SH, Lenze D, Szczepanowski M, Paulsen M, Lipinski S, Russell RB, Adam-Klages S, Apic G, Claviez A, Hasenclever D, Hovestadt V, Hornig N, Korbel JO, Kube D, Langenberger D, Lawerenz C, Lisfeld J, Meyer K, Picelli S, Pischimarov J, Radlwimmer B, Rausch T, Rohde M, Schilhabel M, Scholtysik R, Spang R, Trautmann H, Zenz T, Borkhardt A, Drexler HG, Möller P, MacLeod RAF, Pott C, Schreiber S, Trümper L, Loeffler M, Stadler PS, Lichter P, Eils R, Küppers R, Hummel M, Klapper W, Rosenstiel P, Rosenwald A, Brors B, Siebert R, on behalf of the German ICGC MMML-Seq-Project: 'Recurrent mutation of the ID3 gene in Burkitt Lymphoma identified by integrated genome, exome and transcriptome sequencing', Nature Genetics, 44(12):1316-20. (2012)

  • Fasold M, Binder H: 'Estimating RNA-quality using GeneChip microarrays', BMC Genomics, 13:186. (2012)

  • Langenberger D, Cakir MV, Hoffmann S, Stadler PF: 'Dicer-Processed Small RNAs: Rules and Exceptions', J. Exp. Zool. (Mol. Dev. Evol.) 9999B:1–12. (2012)

  • Langenberger D, Pundhir S, Ekstrom CT, Stadler PF, Hoffmann S, Gorodkin J: 'deepBlockAlign: A tool for aligning RNA-seq profiles of read block patterns', Bioinformatics, 1;28(1):17-24. (2012)

  • Binder H, Fasold M, Hopp L, Cakir V, Bergen Mv, Wirth H: 'Molecular phenotypic portraits - exploring the 'OMES' with individual resolution', Proceedings of HIBIT. (2011)

  • Langenberger D, Bartschat S, Hertel J, Hoffmann S, Tafer H, and Stadler PF: 'Microrna or not microrna?', BSB 2011, Lecture Notes in Computer Science. Springer, pp. 1-9. (2011)

  • Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S: 'DARIO: A ncRNA detection and analysis tool for next-generation sequencing experiments', Nucleic Acids Res. (Web Server Issue), 1-6. (2011)

  • Findeiß S, Langenberger D, Stadler PF, Hoffmann S: 'Traces of Post-Transcriptional RNA Modifications in Deep Sequencing Data', Biol Chem. 392(4):305-313. (2011)

  • Otto C, Hoffmann S, Gorodkin J, Stadler PF: 'Fast local fragment chaining using sum-of-pair gap costs', Algorithms Mol Biol. 6:4.. (2011)

  • Fasold M, Stadler PF, Binder H: 'G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration', BMC Bioinformatics, 11:207. (2010)

  • Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg L, Burt DW, Crasta O, Crooijmans RPMA, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Flicek P, Florea L, Folkerts O, Groenen MAM, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim A, Langenberger D, Lee MK, Lee T, Mane S, Marcais S, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu Z, Van Tassell CP, Vilella AJ, Williams K, Yorke JA, Zhang L, Zhang H, Zhang X, Zhang Y, and Reed KM: 'Multi-platform next generation sequencing of the domestic turkey (Meleagris gallopavo): Genome assembly and analysis.', PLoS Biology. 8,9: e1000475. (2010)

  • Sturm M, Hackenberg M, Langenberger D, Frishman D: 'TargetSpy: a supervised machine learning approach for microRNA target prediction', BMC Bioinformatics. 11(1):292. (2010)

  • Langenberger D, Bermudez-Santana C, Stadler PF, Hoffmann S: 'Identification and Classification of Small RNAs in Transcriptome Sequence Data', Pac Symp Biocomput. 2010:80-7. (2010)

  • Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovitch P, Stadler PF: 'Evidence for Human microRNA-Offset RNAs in Small RNA Sequencing Data', Bioinformatics 25(18):2298-230. (2009)

  • Binder H, Fasold M: 'Mismatch and G-stack modulated probe signals on SNP microarrays', PLoS One, 4(11):e7862. (2009)

  • Hackenberg M, Sturm M, Falcon J, Langenberger D, Aransay A: 'miRanalyzer: A microRNA detection and analysis tool for next-generation sequencing experiments', Nucleic Acids Res. 37(Web Server issue):W68-76. (2009)

  • Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J: 'Fast mapping of short sequences with mismatches, insertions and deletions using index structures', PLoS Comput Biol. 5(9):e1000502.. (2009)

  • Gruen D, Wang YL, Langenberger D, Gunsalus KC, Rajewsky N: 'microRNA Target predictions across seven Drosophial species and comparison to mammalian targets', PLoS Comp. Biol. 1:e13. (2005)