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Items: 1 to 50 of 94

1.

Non-adiabatic effects in the H3+ spectrum.

Amaral PHR, Stanke M, Adamowicz L, Diniz LG, Mohallem JR, Alijah A.

Philos Trans A Math Phys Eng Sci. 2019 Sep 23;377(2154):20180411. doi: 10.1098/rsta.2018.0411. Epub 2019 Aug 5.

PMID:
31378173
2.

Multi-Genome Annotation with AUGUSTUS.

Nachtweide S, Stanke M.

Methods Mol Biol. 2019;1962:139-160. doi: 10.1007/978-1-4939-9173-0_8.

PMID:
31020558
3.

Whole-Genome Annotation with BRAKER.

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

Methods Mol Biol. 2019;1962:65-95. doi: 10.1007/978-1-4939-9173-0_5.

PMID:
31020555
4.

Effects of adult temperature on gene expression in a butterfly: identifying pathways associated with thermal acclimation.

Franke K, Karl I, Centeno TP, Feldmeyer B, Lassek C, Oostra V, Riedel K, Stanke M, Wheat CW, Fischer K.

BMC Evol Biol. 2019 Jan 23;19(1):32. doi: 10.1186/s12862-019-1362-y.

5.

A computational quantum-mechanical model of a molecular magnetic trap.

Adamowicz L, Stanke M, Tellgren E, Helgaker T.

J Chem Phys. 2018 Dec 28;149(24):244112. doi: 10.1063/1.5055767.

PMID:
30599715
6.

Predicting Genes in Single Genomes with AUGUSTUS.

Hoff KJ, Stanke M.

Curr Protoc Bioinformatics. 2019 Mar;65(1):e57. doi: 10.1002/cpbi.57. Epub 2018 Nov 22.

PMID:
30466165
7.

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM.

Nat Genet. 2018 Nov;50(11):1574-1583. doi: 10.1038/s41588-018-0223-8. Epub 2018 Oct 1.

8.

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.

Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B.

Genome Res. 2018 Jul;28(7):1029-1038. doi: 10.1101/gr.233460.117. Epub 2018 Jun 8.

9.

Exome Sequencing Discloses Ionizing-radiation-induced DNA Variants in the Genome of Human Gingiva Fibroblasts.

Nath N, Esche J, Müller J, Jensen LR, Port M, Stanke M, Kaderali L, Scherthan H, Kuss AW.

Health Phys. 2018 Jul;115(1):151-160. doi: 10.1097/HP.0000000000000880.

PMID:
29787441
10.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P.

Genome Res. 2018 Apr;28(4):448-459. doi: 10.1101/gr.234096.117. Epub 2018 Mar 21.

11.

Comparative Genome Annotation.

König S, Romoth L, Stanke M.

Methods Mol Biol. 2018;1704:189-212. doi: 10.1007/978-1-4939-7463-4_6. Review.

PMID:
29277866
12.

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution.

Schwager EE, Sharma PP, Clarke T, Leite DJ, Wierschin T, Pechmann M, Akiyama-Oda Y, Esposito L, Bechsgaard J, Bilde T, Buffry AD, Chao H, Dinh H, Doddapaneni H, Dugan S, Eibner C, Extavour CG, Funch P, Garb J, Gonzalez LB, Gonzalez VL, Griffiths-Jones S, Han Y, Hayashi C, Hilbrant M, Hughes DST, Janssen R, Lee SL, Maeso I, Murali SC, Muzny DM, Nunes da Fonseca R, Paese CLB, Qu J, Ronshaugen M, Schomburg C, Schönauer A, Stollewerk A, Torres-Oliva M, Turetzek N, Vanthournout B, Werren JH, Wolff C, Worley KC, Bucher G, Gibbs RA, Coddington J, Oda H, Stanke M, Ayoub NA, Prpic NM, Flot JF, Posnien N, Richards S, McGregor AP.

BMC Biol. 2017 Jul 31;15(1):62. doi: 10.1186/s12915-017-0399-x.

13.

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 Sep;38(9):1266-1276. doi: 10.1002/humu.23265. Epub 2017 Jun 19.

14.

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.

15.

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.

16.

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
17.

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.

18.

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
19.

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.

20.

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.

21.

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.

22.

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
23.

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.

24.

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
25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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
32.

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.

33.

Automatic control of bioprocesses.

Stanke M, Hitzmann B.

Adv Biochem Eng Biotechnol. 2013;132:35-63. doi: 10.1007/10_2012_167. Review.

PMID:
23307293
34.

Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties.

Martin F, Bovet L, Cordier A, Stanke M, Gunduz I, Peitsch MC, Ivanov NV.

BMC Genomics. 2012 Nov 28;13:674. doi: 10.1186/1471-2164-13-674.

35.

jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus.

Schultz AK, Bulla I, Abdou-Chekaraou M, Gordien E, Morgenstern B, Zoaulim F, Dény P, Stanke M.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W193-8. doi: 10.1093/nar/gks414. Epub 2012 May 16.

36.

Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species.

Raymond F, Boisvert S, Roy G, Ritt JF, Légaré D, Isnard A, Stanke M, Olivier M, Tremblay MJ, Papadopoulou B, Ouellette M, Corbeil J.

Nucleic Acids Res. 2012 Feb;40(3):1131-47. doi: 10.1093/nar/gkr834. Epub 2011 Oct 13.

37.

Flavonoid production in transgenic hop (Humulus lupulus L.) altered by PAP1/MYB75 from Arabidopsis thaliana L.

Gatica-Arias A, Farag MA, Stanke M, Matoušek J, Wessjohann L, Weber G.

Plant Cell Rep. 2012 Jan;31(1):111-9. doi: 10.1007/s00299-011-1144-5. Epub 2011 Sep 13.

PMID:
21912858
38.

Accurate non-Born-Oppenheimer calculations of the complete pure vibrational spectrum of D2 with including relativistic corrections.

Bubin S, Stanke M, Adamowicz L.

J Chem Phys. 2011 Aug 21;135(7):074110. doi: 10.1063/1.3625955.

PMID:
21861559
39.

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown.

Unterthiner T, Schultz AK, Bulla J, Morgenstern B, Stanke M, Bulla I.

BMC Bioinformatics. 2011 Apr 11;12:93. doi: 10.1186/1471-2105-12-93.

40.

Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome.

Specht M, Stanke M, Terashima M, Naumann-Busch B, Janssen I, Höhner R, Hom EF, Liang C, Hippler M.

Proteomics. 2011 May;11(9):1814-23. doi: 10.1002/pmic.201000621. Epub 2011 Mar 22.

41.

Vibrational transitions of the 7LiH+ ion calculated without the Born-Oppenheimer approximation and with leading relativistic corrections.

Bubin S, Stanke M, Adamowicz L.

J Chem Phys. 2011 Jan 14;134(2):024103. doi: 10.1063/1.3525679.

PMID:
21241076
42.

A novel hybrid gene prediction method employing protein multiple sequence alignments.

Keller O, Kollmar M, Stanke M, Waack S.

Bioinformatics. 2011 Mar 15;27(6):757-63. doi: 10.1093/bioinformatics/btr010. Epub 2011 Jan 6.

PMID:
21216780
43.

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.

Arensburger P, Megy K, Waterhouse RM, Abrudan J, Amedeo P, Antelo B, Bartholomay L, Bidwell S, Caler E, Camara F, Campbell CL, Campbell KS, Casola C, Castro MT, Chandramouliswaran I, Chapman SB, Christley S, Costas J, Eisenstadt E, Feschotte C, Fraser-Liggett C, Guigo R, Haas B, Hammond M, Hansson BS, Hemingway J, Hill SR, Howarth C, Ignell R, Kennedy RC, Kodira CD, Lobo NF, Mao C, Mayhew G, Michel K, Mori A, Liu N, Naveira H, Nene V, Nguyen N, Pearson MD, Pritham EJ, Puiu D, Qi Y, Ranson H, Ribeiro JM, Roberston HM, Severson DW, Shumway M, Stanke M, Strausberg RL, Sun C, Sutton G, Tu ZJ, Tubio JM, Unger MF, Vanlandingham DL, Vilella AJ, White O, White JR, Wondji CS, Wortman J, Zdobnov EM, Birren B, Christensen BM, Collins FH, Cornel A, Dimopoulos G, Hannick LI, Higgs S, Lanzaro GC, Lawson D, Lee NH, Muskavitch MA, Raikhel AS, Atkinson PW.

Science. 2010 Oct 1;330(6000):86-8. doi: 10.1126/science.1191864.

44.

Knockdown of tissue nonspecific alkaline phosphatase impairs neural stem cell proliferation and differentiation.

Kermer V, Ritter M, Albuquerque B, Leib C, Stanke M, Zimmermann H.

Neurosci Lett. 2010 Nov 26;485(3):208-11. doi: 10.1016/j.neulet.2010.09.013. Epub 2010 Sep 22.

PMID:
20849921
45.

Draft genome sequence of the oilseed species Ricinus communis.

Chan AP, Crabtree J, Zhao Q, Lorenzi H, Orvis J, Puiu D, Melake-Berhan A, Jones KM, Redman J, Chen G, Cahoon EB, Gedil M, Stanke M, Haas BJ, Wortman JR, Fraser-Liggett CM, Ravel J, Rabinowicz PD.

Nat Biotechnol. 2010 Sep;28(9):951-6. doi: 10.1038/nbt.1674. Epub 2010 Aug 22.

46.

The Amphimedon queenslandica genome and the evolution of animal complexity.

Srivastava M, Simakov O, Chapman J, Fahey B, Gauthier ME, Mitros T, Richards GS, Conaco C, Dacre M, Hellsten U, Larroux C, Putnam NH, Stanke M, Adamska M, Darling A, Degnan SM, Oakley TH, Plachetzki DC, Zhai Y, Adamski M, Calcino A, Cummins SF, Goodstein DM, Harris C, Jackson DJ, Leys SP, Shu S, Woodcroft BJ, Vervoort M, Kosik KS, Manning G, Degnan BM, Rokhsar DS.

Nature. 2010 Aug 5;466(7307):720-6. doi: 10.1038/nature09201.

47.

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).

Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, Canbäck B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigó R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kües U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ.

Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11889-94. doi: 10.1073/pnas.1003391107. Epub 2010 Jun 14.

48.

HIV classification using the coalescent theory.

Bulla I, Schultz AK, Schreiber F, Zhang M, Leitner T, Korber B, Morgenstern B, Stanke M.

Bioinformatics. 2010 Jun 1;26(11):1409-15. doi: 10.1093/bioinformatics/btq159. Epub 2010 Apr 16.

49.

The role of recombination in the emergence of a complex and dynamic HIV epidemic.

Zhang M, Foley B, Schultz AK, Macke JP, Bulla I, Stanke M, Morgenstern B, Korber B, Leitner T.

Retrovirology. 2010 Mar 23;7:25. doi: 10.1186/1742-4690-7-25.

50.

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