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Items: 1 to 20 of 82

1.

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

Cai B, Li B, Kiga N, Thusberg J, Bergquist T, Chen YC, Niknafs N, Carter H, Tokheim C, Beleva-Guthrie V, Douville C, Bhattacharya R, Yeo HTG, Fan J, Sengupta S, Kim D, Cline M, Turner T, Diekhans M, Zaucha J, Pal LR, Cao C, Yu CH, Yin Y, Carraro M, Giollo M, Ferrari C, Leonardi E, Tosatto SCE, Bobe J, Ball M, Hoskins RA, Repo S, Church G, Brenner SE, Moult J, Gough J, Stanke M, Karchin R, Mooney SD.

Hum Mutat. 2017 May 23. doi: 10.1002/humu.23265. [Epub ahead of print]

PMID:
28544481
2.

Wild tobacco genomes reveal the evolution of nicotine biosynthesis.

Xu S, Brockmöller T, Navarro-Quezada A, Kuhl H, Gase K, Ling Z, Zhou W, Kreitzer C, Stanke M, Tang H, Lyons E, Pandey P, Pandey SP, Timmermann B, Gaquerel E, Baldwin IT.

Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):6133-6138. doi: 10.1073/pnas.1700073114. Epub 2017 May 23.

3.

House spider genome uncovers evolutionary shifts in the diversity and expression of black widow venom proteins associated with extreme toxicity.

Gendreau KL, Haney RA, Schwager EE, Wierschin T, Stanke M, Richards S, Garb JE.

BMC Genomics. 2017 Feb 16;18(1):178. doi: 10.1186/s12864-017-3551-7.

4.

Orbit-orbit relativistic correction calculated with all-electron molecular explicitly correlated Gaussians.

Stanke M, Palikot E, Kȩdziera D, Adamowicz L.

J Chem Phys. 2016 Dec 14;145(22):224111.

PMID:
27984888
5.

Simultaneous gene finding in multiple genomes.

König S, Romoth LW, Gerischer L, Stanke M.

Bioinformatics. 2016 Nov 15;32(22):3388-3395. Epub 2016 Jul 27.

PMID:
27466621
6.

Algorithms for calculating mass-velocity and Darwin relativistic corrections with n-electron explicitly correlated Gaussians with shifted centers.

Stanke M, Palikot E, Adamowicz L.

J Chem Phys. 2016 May 7;144(17):174101. doi: 10.1063/1.4947553.

PMID:
27155619
7.

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.

Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M.

Bioinformatics. 2016 Mar 1;32(5):767-9. doi: 10.1093/bioinformatics/btv661. Epub 2015 Nov 11.

PMID:
26559507
8.

Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target.

Ulrich J, Dao VA, Majumdar U, Schmitt-Engel C, Schwirz J, Schultheis D, Ströhlein N, Troelenberg N, Grossmann D, Richter T, Dönitz J, Gerischer L, Leboulle G, Vilcinskas A, Stanke M, Bucher G.

BMC Genomics. 2015 Sep 3;16:674. doi: 10.1186/s12864-015-1880-y.

9.

The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology.

Schmitt-Engel C, Schultheis D, Schwirz J, Ströhlein N, Troelenberg N, Majumdar U, Dao VA, Grossmann D, Richter T, Tech M, Dönitz J, Gerischer L, Theis M, Schild I, Trauner J, Koniszewski ND, Küster E, Kittelmann S, Hu Y, Lehmann S, Siemanowski J, Ulrich J, Panfilio KA, Schröder R, Morgenstern B, Stanke M, Buchhholz F, Frasch M, Roth S, Wimmer EA, Schoppmeier M, Klingler M, Bucher G.

Nat Commun. 2015 Jul 28;6:7822. doi: 10.1038/ncomms8822.

10.

Combining features in a graphical model to predict protein binding sites.

Wierschin T, Wang K, Welter M, Waack S, Stanke M.

Proteins. 2015 May;83(5):844-52. doi: 10.1002/prot.24775. Epub 2015 Mar 14.

PMID:
25663045
11.

Tissue-specific transcriptomics, chromosomal localization, and phylogeny of chemosensory and odorant binding proteins from the red flour beetle Tribolium castaneum reveal subgroup specificities for olfaction or more general functions.

Dippel S, Oberhofer G, Kahnt J, Gerischer L, Opitz L, Schachtner J, Stanke M, Schütz S, Wimmer EA, Angeli S.

BMC Genomics. 2014 Dec 18;15:1141. doi: 10.1186/1471-2164-15-1141.

12.

Non-Born-Oppenheimer calculations of the pure vibrational spectrum of T₂ including relativistic corrections.

Stanke M, Adamowicz L.

J Chem Phys. 2014 Oct 21;141(15):154302. doi: 10.1063/1.4897631.

PMID:
25338891
13.

CRF-based models of protein surfaces improve protein-protein interaction site predictions.

Dong Z, Wang K, Dang TK, Gültas M, Welter M, Wierschin T, Stanke M, Waack S.

BMC Bioinformatics. 2014 Aug 13;15:277. doi: 10.1186/1471-2105-15-277.

14.

The Chlamydomonas genome project: a decade on.

Blaby IK, Blaby-Haas CE, Tourasse N, Hom EF, Lopez D, Aksoy M, Grossman A, Umen J, Dutcher S, Porter M, King S, Witman GB, Stanke M, Harris EH, Goodstein D, Grimwood J, Schmutz J, Vallon O, Merchant SS, Prochnik S.

Trends Plant Sci. 2014 Oct;19(10):672-80. doi: 10.1016/j.tplants.2014.05.008. Epub 2014 Jun 17. Review.

15.

Finding the missing honey bee genes: lessons learned from a genome upgrade.

Elsik CG, Worley KC, Bennett AK, Beye M, Camara F, Childers CP, de Graaf DC, Debyser G, Deng J, Devreese B, Elhaik E, Evans JD, Foster LJ, Graur D, Guigo R; HGSC production teams, Hoff KJ, Holder ME, Hudson ME, Hunt GJ, Jiang H, Joshi V, Khetani RS, Kosarev P, Kovar CL, Ma J, Maleszka R, Moritz RF, Munoz-Torres MC, Murphy TD, Muzny DM, Newsham IF, Reese JT, Robertson HM, Robinson GE, Rueppell O, Solovyev V, Stanke M, Stolle E, Tsuruda JM, Vaerenbergh MV, Waterhouse RM, Weaver DB, Whitfield CW, Wu Y, Zdobnov EM, Zhang L, Zhu D, Gibbs RA; Honey Bee Genome Sequencing Consortium.

BMC Genomics. 2014 Jan 30;15:86. doi: 10.1186/1471-2164-15-86.

16.

Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots.

Tran VT, Braus-Stromeyer SA, Kusch H, Reusche M, Kaever A, Kühn A, Valerius O, Landesfeind M, Aßhauer K, Tech M, Hoff K, Pena-Centeno T, Stanke M, Lipka V, Braus GH.

New Phytol. 2014 Apr;202(2):565-81. doi: 10.1111/nph.12671. Epub 2014 Jan 17.

17.

ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.

Van der Auwera S, Bulla I, Ziller M, Pohlmann A, Harder T, Stanke M.

PLoS One. 2014 Jan 3;9(1):e84558. doi: 10.1371/journal.pone.0084558. eCollection 2014.

18.

WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes.

Hoff KJ, Stanke M.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W123-8. doi: 10.1093/nar/gkt418. Epub 2013 May 21.

19.

Molecular relativistic corrections determined in the framework where the Born-Oppenheimer approximation is not assumed.

Stanke M, Adamowicz L.

J Phys Chem A. 2013 Oct 3;117(39):10129-37. doi: 10.1021/jp4020492. Epub 2013 May 31.

PMID:
23679131
20.

Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.

Schönknecht G, Chen WH, Ternes CM, Barbier GG, Shrestha RP, Stanke M, Bräutigam A, Baker BJ, Banfield JF, Garavito RM, Carr K, Wilkerson C, Rensing SA, Gagneul D, Dickenson NE, Oesterhelt C, Lercher MJ, Weber AP.

Science. 2013 Mar 8;339(6124):1207-10. doi: 10.1126/science.1231707.

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