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Items: 14

1.

An Initial Comparative Genomic Autopsy of Wasting Disease in Sea Stars.

Ruiz-Ramos DV, Schiebelhut LM, Hoff KJ, Wares JP, Dawson MN.

Mol Ecol. 2020 Feb 18. doi: 10.1111/mec.15386. [Epub ahead of print]

PMID:
32069379
2.

MakeHub: Fully Automated Generation of UCSC Genome Browser Assembly Hubs.

Hoff KJ.

Genomics Proteomics Bioinformatics. 2020 Jan 28. pii: S1672-0229(20)30001-2. doi: 10.1016/j.gpb.2019.05.003. [Epub ahead of print]

3.

Non-invasive and label-free 3D-visualization shows in vivo oligomerization of the staphylococcal alkaline shock protein 23 (Asp23).

Petersen I, Schlüter R, Hoff KJ, Liebscher V, Bange G, Riedel K, Pané-Farré J.

Sci Rep. 2020 Jan 10;10(1):125. doi: 10.1038/s41598-019-56907-9.

4.

VARUS: sampling complementary RNA reads from the sequence read archive.

Stanke M, Bruhn W, Becker F, Hoff KJ.

BMC Bioinformatics. 2019 Nov 8;20(1):558. doi: 10.1186/s12859-019-3182-x.

5.

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria.

Philippe H, Poustka AJ, Chiodin M, Hoff KJ, Dessimoz C, Tomiczek B, Schiffer PH, Müller S, Domman D, Horn M, Kuhl H, Timmermann B, Satoh N, Hikosaka-Katayama T, Nakano H, Rowe ML, Elphick MR, Thomas-Chollier M, Hankeln T, Mertes F, Wallberg A, Rast JP, Copley RR, Martinez P, Telford MJ.

Curr Biol. 2019 Jun 3;29(11):1818-1826.e6. doi: 10.1016/j.cub.2019.04.009. Epub 2019 May 16.

PMID:
31104936
6.

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.

7.

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
8.

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.

9.

The nervous system of Xenacoelomorpha: a genomic perspective.

Perea-Atienza E, Gavilán B, Chiodin M, Abril JF, Hoff KJ, Poustka AJ, Martinez P.

J Exp Biol. 2015 Feb 15;218(Pt 4):618-28. doi: 10.1242/jeb.110379.

10.

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.

11.

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.

12.

The effect of sequencing errors on metagenomic gene prediction.

Hoff KJ.

BMC Genomics. 2009 Nov 12;10:520. doi: 10.1186/1471-2164-10-520.

13.

Orphelia: predicting genes in metagenomic sequencing reads.

Hoff KJ, Lingner T, Meinicke P, Tech M.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W101-5. doi: 10.1093/nar/gkp327. Epub 2009 May 8.

14.

Gene prediction in metagenomic fragments: a large scale machine learning approach.

Hoff KJ, Tech M, Lingner T, Daniel R, Morgenstern B, Meinicke P.

BMC Bioinformatics. 2008 Apr 28;9:217. doi: 10.1186/1471-2105-9-217.

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