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Items: 1 to 50 of 631

1.

Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes.

Donath A, Jühling F, Al-Arab M, Bernhart SH, Reinhardt F, Stadler PF, Middendorf M, Bernt M.

Nucleic Acids Res. 2019 Oct 4. pii: gkz833. doi: 10.1093/nar/gkz833. [Epub ahead of print]

PMID:
31584075
2.

Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods.

Drozdova P, Rivarola-Duarte L, Bedulina D, Axenov-Gribanov D, Schreiber S, Gurkov A, Shatilina Z, Vereshchagina K, Lubyaga Y, Madyarova E, Otto C, Jühling F, Busch W, Jakob L, Lucassen M, Sartoris FJ, Hackermüller J, Hoffmann S, Pörtner HO, Luckenbach T, Timofeyev M, Stadler PF.

BMC Genomics. 2019 Sep 13;20(1):712. doi: 10.1186/s12864-019-6024-3.

3.

Selection Pressures on RNA Sequences and Structures.

Nowick K, Walter Costa MB, Höner Zu Siederdissen C, Stadler PF.

Evol Bioinform Online. 2019 Aug 29;15:1176934319871919. doi: 10.1177/1176934319871919. eCollection 2019.

4.

LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3'-CCA end for high-throughput sequencing.

Erber L, Hoffmann A, Fallmann J, Betat H, Stadler PF, Mörl M.

RNA Biol. 2019 Sep 16:1-10. doi: 10.1080/15476286.2019.1664250. [Epub ahead of print]

PMID:
31486704
5.

A streamlined protocol for the detection of mRNA-sRNA interactions using AMT-crosslinking in vitro.

Kirsch R, Olzog VJ, Bonin S, Weinberg CE, Betat H, Stadler PF, Mörl M.

Biotechniques. 2019 Oct;67(4):178-183. doi: 10.2144/btn-2019-0047. Epub 2019 Aug 29.

6.

Concerted Photoluminescence of Electrochemically Self-Assembled CuSCN/Stilbazolium Dye Hybrid Thin Films.

Uda K, Tsuda Y, Okada S, Yamakado R, Sun L, Suzuri Y, White MS, Furis M, Stadler P, Dimitriev O, Yoshida T.

ACS Omega. 2019 Feb 22;4(2):4056-4062. doi: 10.1021/acsomega.8b03632. eCollection 2019 Feb 28.

7.

Molecular cobalt corrole complex for the heterogeneous electrocatalytic reduction of carbon dioxide.

Gonglach S, Paul S, Haas M, Pillwein F, Sreejith SS, Barman S, De R, Müllegger S, Gerschel P, Apfel UP, Coskun H, Aljabour A, Stadler P, Schöfberger W, Roy S.

Nat Commun. 2019 Aug 27;10(1):3864. doi: 10.1038/s41467-019-11868-5.

8.

DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation.

Uxa S, Bernhart SH, Mages CFS, Fischer M, Kohler R, Hoffmann S, Stadler PF, Engeland K, Müller GA.

Nucleic Acids Res. 2019 Sep 26;47(17):9087-9103. doi: 10.1093/nar/gkz635.

9.

Gene expression profile of human T cells following a single stimulation of peripheral blood mononuclear cells with anti-CD3 antibodies.

Sousa IG, Simi KCR, do Almo MM, Bezerra MAG, Doose G, Raiol T, Stadler PF, Hoffmann S, Maranhão AQ, Brigido MM.

BMC Genomics. 2019 Jul 19;20(1):593. doi: 10.1186/s12864-019-5967-8.

10.

Indication of ongoing amphipod speciation in Lake Baikal by genetic structures within endemic species.

Gurkov A, Rivarola-Duarte L, Bedulina D, Fernández Casas I, Michael H, Drozdova P, Nazarova A, Govorukhina E, Timofeyev M, Stadler PF, Luckenbach T.

BMC Evol Biol. 2019 Jul 8;19(1):138. doi: 10.1186/s12862-019-1470-8.

11.

Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods.

Drozdova P, Bedulina D, Madyarova E, Rivarola-Duarte L, Schreiber S, Stadler PF, Luckenbach T, Timofeyev M.

Sci Rep. 2019 Jun 20;9(1):8907. doi: 10.1038/s41598-019-45193-0.

12.

Average Fitness Differences on NK Landscapes.

Hordijk W, Kauffman SA, Stadler PF.

Theory Biosci. 2019 Jun 18. doi: 10.1007/s12064-019-00296-0. [Epub ahead of print]

PMID:
31214941
13.

Exploration of the chemical space and its three historical regimes.

Llanos EJ, Leal W, Luu DH, Jost J, Stadler PF, Restrepo G.

Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):12660-12665. doi: 10.1073/pnas.1816039116. Epub 2019 Jun 11. Erratum in: Proc Natl Acad Sci U S A. 2019 Jul 8;:.

PMID:
31186353
14.

Persistent radical anions in the series of peri-arylenes: broadband light absorption until far in the NIR and purely organic magnetism.

Langhals H, Ritter-Faizade U, Stadler P, Havlicek M, Hofer A, Sariciftci NS.

Monatsh Chem. 2019;150(5):885-900. doi: 10.1007/s00706-019-02404-8. Epub 2019 May 2.

15.

Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541-750).

Keller M, Spyrou MA, Scheib CL, Neumann GU, Kröpelin A, Haas-Gebhard B, Päffgen B, Haberstroh J, Ribera I Lacomba A, Raynaud C, Cessford C, Durand R, Stadler P, Nägele K, Bates JS, Trautmann B, Inskip SA, Peters J, Robb JE, Kivisild T, Castex D, McCormick M, Bos KI, Harbeck M, Herbig A, Krause J.

Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12363-12372. doi: 10.1073/pnas.1820447116. Epub 2019 Jun 4.

16.

The RNA workbench 2.0: next generation RNA data analysis.

Fallmann J, Videm P, Bagnacani A, Batut B, Doyle MA, Klingstrom T, Eggenhofer F, Stadler PF, Backofen R, Grüning B.

Nucleic Acids Res. 2019 Jul 2;47(W1):W511-W515. doi: 10.1093/nar/gkz353.

17.

Abdominal aortic aneurysm as an IgG4-related disease.

Prucha M, Sedivy P, Stadler P, Zdrahal P, Prokopova P, Voska L, Sedlackova L.

Clin Exp Immunol. 2019 Sep;197(3):361-365. doi: 10.1111/cei.13307. Epub 2019 May 14.

18.

Automatic Curation of Large Comparative Animal MicroRNA Data Sets.

Yazbeck AM, Stadler PF, Tout K, Fallmann J.

Bioinformatics. 2019 Apr 16. pii: btz271. doi: 10.1093/bioinformatics/btz271. [Epub ahead of print]

PMID:
30993337
19.

Ryūtō: network-flow based transcriptome reconstruction.

Gatter T, Stadler PF.

BMC Bioinformatics. 2019 Apr 16;20(1):190. doi: 10.1186/s12859-019-2786-5.

20.

Best match graphs.

Geiß M, Chávez E, González Laffitte M, López Sánchez A, Stadler BMR, Valdivia DI, Hellmuth M, Hernández Rosales M, Stadler PF.

J Math Biol. 2019 Jun;78(7):2015-2057. doi: 10.1007/s00285-019-01332-9. Epub 2019 Apr 9.

21.

Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma.

López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, Waszak SM, Huang Z, Sieverling L, Paramasivam N, Seufert J, Sungalee S, Russell RB, Bausinger J, Kretzmer H, Ammerpohl O, Bergmann AK, Binder H, Borkhardt A, Brors B, Claviez A, Doose G, Feuerbach L, Haake A, Hansmann ML, Hoell J, Hummel M, Korbel JO, Lawerenz C, Lenze D, Radlwimmer B, Richter J, Rosenstiel P, Rosenwald A, Schilhabel MB, Stein H, Stilgenbauer S, Stadler PF, Szczepanowski M, Weniger MA, Zapatka M, Eils R, Lichter P, Loeffler M, Möller P, Trümper L, Klapper W; ICGC MMML-Seq Consortium, Hoffmann S, Küppers R, Burkhardt B, Schlesner M, Siebert R.

Nat Commun. 2019 Mar 29;10(1):1459. doi: 10.1038/s41467-019-08578-3.

22.

Photoconductive Properties of Dibenzotetrathiafulvalene-Tetracyanoquinodimethane (DBTTF-TCNQ) Nanorods Prepared by the Reprecipitation Method.

Takeda M, Hojo K, Umemoto K, Scharber MC, Stadler P, Yumusak C, Sariciftci NS, White MS, Furis M, Okada S, Yoshida T, Matsui J, Masuhara A.

J Nanosci Nanotechnol. 2019 Aug 1;19(8):4599-4602. doi: 10.1166/jnn.2019.16346.

PMID:
30913754
23.

Gene expression in patients with abdominal aortic aneurysm - more than immunological mechanisms involved.

Prucha M, Sedivy P, Stadler P, Zdrahal P, Matoska V, Strnad H.

Physiol Res. 2019 Jun 30;68(3):385-394. Epub 2019 Mar 22.

24.

SSS-test: a novel test for detecting positive selection on RNA secondary structure.

Walter Costa MB, Höner Zu Siederdissen C, Dunjić M, Stadler PF, Nowick K.

BMC Bioinformatics. 2019 Mar 21;20(1):151. doi: 10.1186/s12859-019-2711-y.

25.

Spring Water of an Alpine Karst Aquifer Is Dominated by a Taxonomically Stable but Discharge-Responsive Bacterial Community.

Savio D, Stadler P, Reischer GH, Demeter K, Linke RB, Blaschke AP, Mach RL, Kirschner AKT, Stadler H, Farnleitner AH.

Front Microbiol. 2019 Feb 15;10:28. doi: 10.3389/fmicb.2019.00028. eCollection 2019.

26.

Event-transport of beta-d-glucuronidase in an agricultural headwater stream: Assessment of seasonal patterns by on-line enzymatic activity measurements and environmental isotopes.

Stadler P, Blöschl G, Nemeth L, Oismüller M, Kumpan M, Krampe J, Farnleitner AH, Zessner M.

Sci Total Environ. 2019 Apr 20;662:236-245. doi: 10.1016/j.scitotenv.2019.01.143. Epub 2019 Jan 15.

PMID:
30690358
27.

Current vascular allograft procurement, cryopreservation and transplantation techniques in the Czech Republic.

Špaček M, Měřička P, Janoušek L, Štádler P, Adamec M, Vlachovský R, Guňka I, Navrátil P, Thieme F, Špunda R, Burkert J, Staffa R, Němec P, Lindner J.

Adv Clin Exp Med. 2019 Apr;28(4):529-534. doi: 10.17219/acem/90037.

28.

Conditional cash transfers to prevent mother-to-child transmission in low facility-delivery settings: evidence from a randomised controlled trial in Nigeria.

Liu JX, Shen J, Wilson N, Janumpalli S, Stadler P, Padian N.

BMC Pregnancy Childbirth. 2019 Jan 16;19(1):32. doi: 10.1186/s12884-019-2172-3.

29.

Identification and characterization of novel conserved RNA structures in Drosophila.

Kirsch R, Seemann SE, Ruzzo WL, Cohen SM, Stadler PF, Gorodkin J.

BMC Genomics. 2018 Dec 11;19(1):899. doi: 10.1186/s12864-018-5234-4.

30.

Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation.

Kolora SRR, Weigert A, Saffari A, Kehr S, Walter Costa MB, Spröer C, Indrischek H, Chintalapati M, Lohse K, Doose G, Overmann J, Bunk B, Bleidorn C, Grimm-Seyfarth A, Henle K, Nowick K, Faria R, Stadler PF, Schlegel M.

Gigascience. 2019 Feb 1;8(2). pii: giy160. doi: 10.1093/gigascience/giy160.

31.

Superbubbles revisited.

Gärtner F, Müller L, Stadler PF.

Algorithms Mol Biol. 2018 Dec 1;13:16. doi: 10.1186/s13015-018-0134-3. eCollection 2018.

32.

Patterning the insect eye: From stochastic to deterministic mechanisms.

Ebadi H, Perry M, Short K, Klemm K, Desplan C, Stadler PF, Mehta A.

PLoS Comput Biol. 2018 Nov 15;14(11):e1006363. doi: 10.1371/journal.pcbi.1006363. eCollection 2018 Nov.

33.

Spatial patterns of enzymatic activity in large water bodies: Ship-borne measurements of beta-D-glucuronidase activity as a rapid indicator of microbial water quality.

Stadler P, Loken LC, Crawford JT, Schramm PJ, Sorsa K, Kuhn C, Savio D, Striegl RG, Butman D, Stanley EH, Farnleitner AH, Zessner M.

Sci Total Environ. 2019 Feb 15;651(Pt 2):1742-1752. doi: 10.1016/j.scitotenv.2018.10.084. Epub 2018 Oct 8.

34.

Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis.

Kutsche LK, Gysi DM, Fallmann J, Lenk K, Petri R, Swiersy A, Klapper SD, Pircs K, Khattak S, Stadler PF, Jakobsson J, Nowick K, Busskamp V.

Cell Syst. 2018 Oct 24;7(4):438-452.e8. doi: 10.1016/j.cels.2018.08.011. Epub 2018 Oct 3.

35.

Coordinate systems for supergenomes.

Gärtner F, Höner Zu Siederdissen C, Müller L, Stadler PF.

Algorithms Mol Biol. 2018 Sep 24;13:15. doi: 10.1186/s13015-018-0133-4. eCollection 2018.

36.

RNApuzzler: efficient outerplanar drawing of RNA-secondary structures.

Wiegreffe D, Alexander D, Stadler PF, Zeckzer D.

Bioinformatics. 2019 Apr 15;35(8):1342-1349. doi: 10.1093/bioinformatics/bty817.

PMID:
30239566
37.

Beyond the 3'UTR binding-microRNA-induced protein truncation via DNA binding.

von Brandenstein M, Bernhart SH, Pansky A, Richter C, Kohl T, Deckert M, Heidenreich A, Stadler PF, Montesinos-Rongen M, Fries JWU.

Oncotarget. 2018 Aug 28;9(67):32855-32867. doi: 10.18632/oncotarget.26023. eCollection 2018 Aug 28.

38.

Noncoding RNA Transcripts during Differentiation of Induced Pluripotent Stem Cells into Hepatocytes.

Skrzypczyk A, Kehr S, Krystel I, Bernhart SH, Giri S, Bader A, Stadler PF.

Stem Cells Int. 2018 Aug 19;2018:5692840. doi: 10.1155/2018/5692840. eCollection 2018.

39.

Nonprotein-Coding RNAs as Regulators of Development in Tunicates.

Velandia-Huerto CA, Brown FD, Gittenberger A, Stadler PF, Bermúdez-Santana CI.

Results Probl Cell Differ. 2018;65:197-225. doi: 10.1007/978-3-319-92486-1_11. Review.

PMID:
30083922
40.

The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments.

Wiegreffe D, Müller L, Steuck J, Zeckzer D, Stadler PF.

BMC Res Notes. 2018 Jul 28;11(1):512. doi: 10.1186/s13104-018-3633-x.

41.

TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes.

Waldl M, Thiel BC, Ochsenreiter R, Holzenleiter A, de Araujo Oliveira JV, Walter MEMT, Wolfinger MT, Stadler PF.

Genes (Basel). 2018 Jul 26;9(8). pii: E372. doi: 10.3390/genes9080372.

42.

Trichoplax genomes reveal profound admixture and suggest stable wild populations without bisexual reproduction.

Kamm K, Osigus HJ, Stadler PF, DeSalle R, Schierwater B.

Sci Rep. 2018 Jul 24;8(1):11168. doi: 10.1038/s41598-018-29400-y.

43.

Split-inducing indels in phylogenomic analysis.

Donath A, Stadler PF.

Algorithms Mol Biol. 2018 Jul 16;13:12. doi: 10.1186/s13015-018-0130-7. eCollection 2018.

44.

Chemical Transformation Motifs-Modelling Pathways as Integer Hyperflows.

Andersen JL, Flamm C, Merkle D, Stadler PF.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Mar-Apr;16(2):510-523. doi: 10.1109/TCBB.2017.2781724. Epub 2017 Dec 11.

PMID:
29990045
45.

Reconstructing gene trees from Fitch's xenology relation.

Geiß M, Anders J, Stadler PF, Wieseke N, Hellmuth M.

J Math Biol. 2018 Nov;77(5):1459-1491. doi: 10.1007/s00285-018-1260-8. Epub 2018 Jun 27.

PMID:
29951855
46.

Cover-Encodings of Fitness Landscapes.

Klemm K, Mehta A, Stadler PF.

Bull Math Biol. 2018 Aug;80(8):2154-2176. doi: 10.1007/s11538-018-0451-1. Epub 2018 Jun 12.

47.

Phylogenetics beyond biology.

Retzlaff N, Stadler PF.

Theory Biosci. 2018 Nov;137(2):133-143. doi: 10.1007/s12064-018-0264-7. Epub 2018 Jun 21.

48.

Opening the black box of spring water microbiology from alpine karst aquifers to support proactive drinking water resource management.

Savio D, Stadler P, Reischer GH, Kirschner AKT, Demeter K, Linke R, Blaschke AP, Sommer R, Szewzyk U, Wilhartitz IC, Mach RL, Stadler H, Farnleitner AH.

WIREs Water. 2018 May-Jun;5(3):e1282. doi: 10.1002/wat2.1282. Epub 2018 Mar 9. Review.

49.

Rare Splice Variants in Long Non-Coding RNAs.

Sen R, Doose G, Stadler PF.

Noncoding RNA. 2017 Jul 5;3(3). pii: E23. doi: 10.3390/ncrna3030023.

50.

In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors.

Sutandy FXR, Ebersberger S, Huang L, Busch A, Bach M, Kang HS, Fallmann J, Maticzka D, Backofen R, Stadler PF, Zarnack K, Sattler M, Legewie S, König J.

Genome Res. 2018 May;28(5):699-713. doi: 10.1101/gr.229757.117. Epub 2018 Apr 11.

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