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Items: 1 to 20 of 357

1.

Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits.

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

Sci Rep. 2019 Nov 26;9(1):17561. doi: 10.1038/s41598-019-54037-w.

2.

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.

Corrêa FB, Saraiva JP, Stadler PF, da Rocha UN.

Nucleic Acids Res. 2019 Nov 15. pii: gkz994. doi: 10.1093/nar/gkz994. [Epub ahead of print]

PMID:
31728526
3.

Transcriptome-level effects of the model organic pollutant phenanthrene and its solvent acetone in three amphipod species.

Shatilina Z, Drozdova P, Bedulina D, Rivarola-Duarte L, Schreiber S, Otto C, Jühling F, Aulhorn S, Busch W, Lubyaga Y, Kondrateva E, Pobezhimova T, Jakob L, Lucassen M, Sartoris FJ, Hackermüller J, Pörtner HO, Stadler PF, Luckenbach T, Timofeyev M.

Comp Biochem Physiol Part D Genomics Proteomics. 2019 Oct 31;33:100630. doi: 10.1016/j.cbd.2019.100630. [Epub ahead of print]

PMID:
31710888
4.

Reciprocal best match graphs.

Geiß M, Stadler PF, Hellmuth M.

J Math Biol. 2019 Oct 30. doi: 10.1007/s00285-019-01444-2. [Epub ahead of print]

PMID:
31691135
5.

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 Nov 18;47(20):10543-10552. doi: 10.1093/nar/gkz833.

6.

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.

7.

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.

8.

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
9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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
15.

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
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.

Automatic curation of large comparative animal MicroRNA datasets.

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

Bioinformatics. 2019 Nov 1;35(22):4553-4559. doi: 10.1093/bioinformatics/btz271.

PMID:
30993337
18.

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.

19.

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.

20.

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.

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