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Items: 1 to 50 of 149

1.

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.

Neumann T, Herzog VA, Muhar M, von Haeseler A, Zuber J, Ameres SL, Rescheneder P.

BMC Bioinformatics. 2019 May 20;20(1):258. doi: 10.1186/s12859-019-2849-7.

2.

Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity.

Schrempf D, Minh BQ, von Haeseler A, Kosiol C.

Mol Biol Evol. 2019 Jun 1;36(6):1294-1301. doi: 10.1093/molbev/msz043.

3.

Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase.

Schenk S, Bannister SC, Sedlazeck FJ, Anrather D, Minh BQ, Bileck A, Hartl M, von Haeseler A, Gerner C, Raible F, Tessmar-Raible K.

Elife. 2019 Feb 15;8. pii: e41556. doi: 10.7554/eLife.41556.

4.

VARIFI-Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data.

Krunic M, Venhuizen P, Müllauer L, Kaserer B, von Haeseler A.

J Pers Med. 2019 Feb 1;9(1). pii: E10. doi: 10.3390/jpm9010010.

5.

The Evolutionary Traceability of a Protein.

Jain A, Perisa D, Fliedner F, von Haeseler A, Ebersberger I.

Genome Biol Evol. 2019 Feb 1;11(2):531-545. doi: 10.1093/gbe/evz008.

6.

Accurate detection of complex structural variations using single-molecule sequencing.

Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC.

Nat Methods. 2018 Jun;15(6):461-468. doi: 10.1038/s41592-018-0001-7. Epub 2018 Apr 30.

7.

In vivo insertion pool sequencing identifies virulence factors in a complex fungal-host interaction.

Uhse S, Pflug FG, Stirnberg A, Ehrlinger K, von Haeseler A, Djamei A.

PLoS Biol. 2018 Apr 23;16(4):e2005129. doi: 10.1371/journal.pbio.2005129. eCollection 2018 Apr.

8.

TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers.

Pflug FG, von Haeseler A.

Bioinformatics. 2018 Sep 15;34(18):3137-3144. doi: 10.1093/bioinformatics/bty283.

9.

Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes.

Alves RJE, Minh BQ, Urich T, von Haeseler A, Schleper C.

Nat Commun. 2018 Apr 17;9(1):1517. doi: 10.1038/s41467-018-03861-1.

10.

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis.

Muhar M, Ebert A, Neumann T, Umkehrer C, Jude J, Wieshofer C, Rescheneder P, Lipp JJ, Herzog VA, Reichholf B, Cisneros DA, Hoffmann T, Schlapansky MF, Bhat P, von Haeseler A, Köcher T, Obenauf AC, Popow J, Ameres SL, Zuber J.

Science. 2018 May 18;360(6390):800-805. doi: 10.1126/science.aao2793. Epub 2018 Apr 5.

11.

Germline Variants in the POT1-Gene in High-Risk Melanoma Patients in Austria.

Müller C, Krunic M, Wendt J, von Haeseler A, Okamoto I.

G3 (Bethesda). 2018 May 4;8(5):1475-1480. doi: 10.1534/g3.117.300394.

12.

MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.

Hoang DT, Vinh LS, Flouri T, Stamatakis A, von Haeseler A, Minh BQ.

BMC Evol Biol. 2018 Feb 2;18(1):11. doi: 10.1186/s12862-018-1131-3.

13.

Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model.

Nguyen LT, von Haeseler A, Minh BQ.

Syst Biol. 2018 May 1;67(3):552-558. doi: 10.1093/sysbio/syx092.

14.

UFBoot2: Improving the Ultrafast Bootstrap Approximation.

Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS.

Mol Biol Evol. 2018 Feb 1;35(2):518-522. doi: 10.1093/molbev/msx281.

15.

Thiol-linked alkylation of RNA to assess expression dynamics.

Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J, Ameres SL.

Nat Methods. 2017 Dec;14(12):1198-1204. doi: 10.1038/nmeth.4435. Epub 2017 Sep 25.

16.

HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.

Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C.

AIDS Res Hum Retroviruses. 2017 Nov;33(11):1083-1098. doi: 10.1089/AID.2017.0061. Epub 2017 May 25.

17.

ModelFinder: fast model selection for accurate phylogenetic estimates.

Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS.

Nat Methods. 2017 Jun;14(6):587-589. doi: 10.1038/nmeth.4285. Epub 2017 May 8.

18.

The genomic basis of circadian and circalunar timing adaptations in a midge.

Kaiser TS, Poehn B, Szkiba D, Preussner M, Sedlazeck FJ, Zrim A, Neumann T, Nguyen LT, Betancourt AJ, Hummel T, Vogel H, Dorner S, Heyd F, von Haeseler A, Tessmar-Raible K.

Nature. 2016 Dec 1;540(7631):69-73. doi: 10.1038/nature20151. Epub 2016 Nov 21.

19.

Reversible polymorphism-aware phylogenetic models and their application to tree inference.

Schrempf D, Minh BQ, De Maio N, von Haeseler A, Kosiol C.

J Theor Biol. 2016 Oct 21;407:362-370. doi: 10.1016/j.jtbi.2016.07.042. Epub 2016 Jul 29.

20.

Next-generation sequencing diagnostics of bacteremia in septic patients.

Grumaz S, Stevens P, Grumaz C, Decker SO, Weigand MA, Hofer S, Brenner T, von Haeseler A, Sohn K.

Genome Med. 2016 Jul 1;8(1):73. doi: 10.1186/s13073-016-0326-8.

21.

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices.

Chernomor O, von Haeseler A, Minh BQ.

Syst Biol. 2016 Nov;65(6):997-1008. Epub 2016 Apr 26.

22.

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.

Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ.

Nucleic Acids Res. 2016 Jul 8;44(W1):W232-5. doi: 10.1093/nar/gkw256. Epub 2016 Apr 15.

23.

Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance.

Jagut M, Hamminger P, Woglar A, Millonigg S, Paulin L, Mikl M, Dello Stritto MR, Tang L, Habacher C, Tam A, Gallach M, von Haeseler A, Villeneuve AM, Jantsch V.

PLoS Biol. 2016 Mar 24;14(3):e1002412. doi: 10.1371/journal.pbio.1002412. eCollection 2016 Mar.

24.

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha.

Gesson K, Rescheneder P, Skoruppa MP, von Haeseler A, Dechat T, Foisner R.

Genome Res. 2016 Apr;26(4):462-73. doi: 10.1101/gr.196220.115. Epub 2016 Jan 21.

25.

Teaser: Individualized benchmarking and optimization of read mapping results for NGS data.

Smolka M, Rescheneder P, Schatz MC, von Haeseler A, Sedlazeck FJ.

Genome Biol. 2015 Oct 22;16:235. doi: 10.1186/s13059-015-0803-1.

26.

The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways.

Tscherner M, Zwolanek F, Jenull S, Sedlazeck FJ, Petryshyn A, Frohner IE, Mavrianos J, Chauhan N, von Haeseler A, Kuchler K.

PLoS Pathog. 2015 Oct 16;11(10):e1005218. doi: 10.1371/journal.ppat.1005218. eCollection 2015 Oct.

27.

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

Chernomor O, Minh BQ, von Haeseler A.

J Comput Biol. 2015 Dec;22(12):1129-42. doi: 10.1089/cmb.2015.0146. Epub 2015 Oct 8.

28.

Split diversity in constrained conservation prioritization using integer linear programming.

Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger M, von Haeseler A.

Methods Ecol Evol. 2015 Jan;6(1):83-91. Epub 2014 Dec 6.

29.

Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study.

Krunic M, Ertl R, Hagen B, Sedlazeck FJ, Hofmann-Lehmann R, von Haeseler A, Klein D.

BMC Vet Res. 2015 Apr 10;11:90. doi: 10.1186/s12917-015-0378-9.

30.

Innate immune response to Streptococcus pyogenes depends on the combined activation of TLR13 and TLR2.

Fieber C, Janos M, Koestler T, Gratz N, Li XD, Castiglia V, Aberle M, Sauert M, Wegner M, Alexopoulou L, Kirschning CJ, Chen ZJ, von Haeseler A, Kovarik P.

PLoS One. 2015 Mar 10;10(3):e0119727. doi: 10.1371/journal.pone.0119727. eCollection 2015.

31.

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.

Chipman AD, Ferrier DE, Brena C, Qu J, Hughes DS, Schröder R, Torres-Oliva M, Znassi N, Jiang H, Almeida FC, Alonso CR, Apostolou Z, Aqrawi P, Arthur W, Barna JC, Blankenburg KP, Brites D, Capella-Gutiérrez S, Coyle M, Dearden PK, Du Pasquier L, Duncan EJ, Ebert D, Eibner C, Erikson G, Evans PD, Extavour CG, Francisco L, Gabaldón T, Gillis WJ, Goodwin-Horn EA, Green JE, Griffiths-Jones S, Grimmelikhuijzen CJ, Gubbala S, Guigó R, Han Y, Hauser F, Havlak P, Hayden L, Helbing S, Holder M, Hui JH, Hunn JP, Hunnekuhl VS, Jackson L, Javaid M, Jhangiani SN, Jiggins FM, Jones TE, Kaiser TS, Kalra D, Kenny NJ, Korchina V, Kovar CL, Kraus FB, Lapraz F, Lee SL, Lv J, Mandapat C, Manning G, Mariotti M, Mata R, Mathew T, Neumann T, Newsham I, Ngo DN, Ninova M, Okwuonu G, Ongeri F, Palmer WJ, Patil S, Patraquim P, Pham C, Pu LL, Putman NH, Rabouille C, Ramos OM, Rhodes AC, Robertson HE, Robertson HM, Ronshaugen M, Rozas J, Saada N, Sánchez-Gracia A, Scherer SE, Schurko AM, Siggens KW, Simmons D, Stief A, Stolle E, Telford MJ, Tessmar-Raible K, Thornton R, van der Zee M, von Haeseler A, Williams JM, Willis JH, Wu Y, Zou X, Lawson D, Muzny DM, Worley KC, Gibbs RA, Akam M, Richards S.

PLoS Biol. 2014 Nov 25;12(11):e1002005. doi: 10.1371/journal.pbio.1002005. eCollection 2014 Nov.

32.

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.

Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ.

Mol Biol Evol. 2015 Jan;32(1):268-74. doi: 10.1093/molbev/msu300. Epub 2014 Nov 3.

33.

The phylogenetic likelihood library.

Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer AJ, Nguyen LT, Minh BQ, Von Haeseler A, Stamatakis A.

Syst Biol. 2015 Mar;64(2):356-62. doi: 10.1093/sysbio/syu084. Epub 2014 Oct 30.

34.

ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain.

Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, von Haeseler A, Jantsch MF.

Nucleic Acids Res. 2014 Oct 29;42(19):12155-68. doi: 10.1093/nar/gku844. Epub 2014 Sep 26.

35.

A SAGE based approach to human glomerular endothelium: defining the transcriptome, finding a novel molecule and highlighting endothelial diversity.

Sengoelge G, Winnicki W, Kupczok A, von Haeseler A, Schuster M, Pfaller W, Jennings P, Weltermann A, Blake S, Sunder-Plassmann G.

BMC Genomics. 2014 Aug 27;15:725. doi: 10.1186/1471-2164-15-725.

36.

Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria.

Kaschner M, Loeschcke A, Krause J, Minh BQ, Heck A, Endres S, Svensson V, Wirtz A, von Haeseler A, Jaeger KE, Drepper T, Krauss U.

Mol Microbiol. 2014 Sep;93(5):1066-78. doi: 10.1111/mmi.12719. Epub 2014 Aug 5.

37.

SNP2GO: functional analysis of genome-wide association studies.

Szkiba D, Kapun M, von Haeseler A, Gallach M.

Genetics. 2014 May;197(1):285-9. doi: 10.1534/genetics.113.160341. Epub 2014 Feb 21.

38.

The evolution of the ribosome biogenesis pathway from a yeast perspective.

Ebersberger I, Simm S, Leisegang MS, Schmitzberger P, Mirus O, von Haeseler A, Bohnsack MT, Schleiff E.

Nucleic Acids Res. 2014 Feb;42(3):1509-23. doi: 10.1093/nar/gkt1137. Epub 2013 Nov 14.

39.

Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects.

Dell'Ampio E, Meusemann K, Szucsich NU, Peters RS, Meyer B, Borner J, Petersen M, Aberer AJ, Stamatakis A, Walzl MG, Minh BQ, von Haeseler A, Ebersberger I, Pass G, Misof B.

Mol Biol Evol. 2014 Jan;31(1):239-49. doi: 10.1093/molbev/mst196. Epub 2013 Oct 18.

40.

NextGenMap: fast and accurate read mapping in highly polymorphic genomes.

Sedlazeck FJ, Rescheneder P, von Haeseler A.

Bioinformatics. 2013 Nov 1;29(21):2790-1. doi: 10.1093/bioinformatics/btt468. Epub 2013 Aug 23.

PMID:
23975764
41.

State-of the art methodologies dictate new standards for phylogenetic analysis.

Anisimova M, Liberles DA, Philippe H, Provan J, Pupko T, von Haeseler A.

BMC Evol Biol. 2013 Aug 1;13:161. doi: 10.1186/1471-2148-13-161. Review.

42.

Exploring the sampling universe of RNA-seq.

Tauber S, von Haeseler A.

Stat Appl Genet Mol Biol. 2013 Apr 16;12(2):175-88. doi: 10.1515/sagmb-2012-0049.

PMID:
23629158
43.

Updating benchtop sequencing performance comparison.

Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U, Kalinowski J, Mellmann A, Goesmann A, von Haeseler A, Stoye J, Harmsen D.

Nat Biotechnol. 2013 Apr;31(4):294-6. doi: 10.1038/nbt.2522. No abstract available. Erratum in: Nat Biotechnol. 2013 Dec;31(12):1148.

PMID:
23563421
44.

Ultrafast approximation for phylogenetic bootstrap.

Minh BQ, Nguyen MA, von Haeseler A.

Mol Biol Evol. 2013 May;30(5):1188-95. doi: 10.1093/molbev/mst024. Epub 2013 Feb 15.

45.

Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets.

Sedlazeck FJ, Talloji P, von Haeseler A, Bachmair A.

Genomics. 2013 Mar;101(3):204-9. doi: 10.1016/j.ygeno.2012.12.001. Epub 2012 Dec 12.

46.

On the group theoretical background of assigning stepwise mutations onto phylogenies.

Fischer M, Klaere S, Thi Nguyen MA, von Haeseler A.

Algorithms Mol Biol. 2012 Dec 15;7(1):36. doi: 10.1186/1748-7188-7-36.

47.

NGC: lossless and lossy compression of aligned high-throughput sequencing data.

Popitsch N, von Haeseler A.

Nucleic Acids Res. 2013 Jan 7;41(1):e27. doi: 10.1093/nar/gks939. Epub 2012 Oct 12.

48.

Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis.

Dinh HQ, Dubin M, Sedlazeck FJ, Lettner N, Mittelsten Scheid O, von Haeseler A.

PLoS One. 2012;7(7):e41528. doi: 10.1371/journal.pone.0041528. Epub 2012 Jul 20.

49.

TreeSnatcher plus: capturing phylogenetic trees from images.

Laubach T, von Haeseler A, Lercher MJ.

BMC Bioinformatics. 2012 May 24;13:110. doi: 10.1186/1471-2105-13-110.

50.

Identification of an ancient haemophilia A splice site mutation.

Reitter-Pfoertner S, von Haeseler A, Horvath B, Sunder-Plassmann R, Tiedje V, Pabinger I, Mannhalter C.

Thromb Res. 2012 Sep;130(3):445-50. doi: 10.1016/j.thromres.2012.02.008. Epub 2012 Mar 6.

PMID:
22401796

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