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Items: 1 to 20 of 168

1.

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.

2.

Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtii.

Allmer J, Naumann B, Markert C, Zhang M, Hippler M.

Proteomics. 2006 Dec;6(23):6207-20.

PMID:
17078018
4.

Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics.

Ding J, Li X, Hu H.

Plant Physiol. 2012 Oct;160(2):613-23. doi: 10.1104/pp.112.200840. Epub 2012 Aug 22.

5.

Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii.

May P, Wienkoop S, Kempa S, Usadel B, Christian N, Rupprecht J, Weiss J, Recuenco-Munoz L, Ebenhöh O, Weckwerth W, Walther D.

Genetics. 2008 May;179(1):157-66. doi: 10.1534/genetics.108.088336.

6.

AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome.

Stanke M, Tzvetkova A, Morgenstern B.

Genome Biol. 2006;7 Suppl 1:S11.1-8. Epub 2006 Aug 7.

7.

A proteogenomic survey of the Medicago truncatula genome.

Volkening JD, Bailey DJ, Rose CM, Grimsrud PA, Howes-Podoll M, Venkateshwaran M, Westphall MS, Ané JM, Coon JJ, Sussman MR.

Mol Cell Proteomics. 2012 Oct;11(10):933-44. Epub 2012 Jul 5.

8.

Improving gene-finding in Chlamydomonas reinhardtii:GreenGenie2.

Kwan AL, Li L, Kulp DC, Dutcher SK, Stormo GD.

BMC Genomics. 2009 May 7;10:210. doi: 10.1186/1471-2164-10-210.

10.

Integrating alternative splicing detection into gene prediction.

Foissac S, Schiex T.

BMC Bioinformatics. 2005 Feb 10;6:25.

11.

Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii.

Labadorf A, Link A, Rogers MF, Thomas J, Reddy AS, Ben-Hur A.

BMC Genomics. 2010 Feb 17;11:114. doi: 10.1186/1471-2164-11-114.

12.

The different proteomes of Chlamydomonas reinhardtii.

Valledor L, Recuenco-Munoz L, Egelhofer V, Wienkoop S, Weckwerth W.

J Proteomics. 2012 Oct 22;75(18):5883-7. doi: 10.1016/j.jprot.2012.07.045. Epub 2012 Aug 7.

PMID:
22967953
13.

Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.

Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S.

J Proteomics. 2013 Jun 28;86:27-42. doi: 10.1016/j.jprot.2013.04.036. Epub 2013 May 9.

PMID:
23665149
14.

Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species.

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

BMC Bioinformatics. 2008 Jun 13;9:278. doi: 10.1186/1471-2105-9-278.

15.

Chlamydomonas reinhardtii proteomics.

Stauber EJ, Hippler M.

Plant Physiol Biochem. 2004 Dec;42(12):989-1001. Epub 2005 Jan 18. Review.

PMID:
15707836
16.
17.

Gene model detection using mass spectrometry.

Nanduri B, Wang N, Lawrence ML, Bridges SM, Burgess SC.

Methods Mol Biol. 2010;604:137-44. doi: 10.1007/978-1-60761-444-9_10.

PMID:
20013369
18.

Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation.

Kumar D, Yadav AK, Jia X, Mulvenna J, Dash D.

Mol Cell Proteomics. 2016 Jan;15(1):329-39. doi: 10.1074/mcp.M114.047126. Epub 2015 Nov 11.

19.

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.

20.

Patching Holes in the Chlamydomonas Genome.

Tulin F, Cross FR.

G3 (Bethesda). 2016 Jul 7;6(7):1899-910. doi: 10.1534/g3.116.029207.

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