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Items: 20

1.

EPIFANY: A Method for Efficient High-Confidence Protein Inference.

Pfeuffer J, Sachsenberg T, Dijkstra TMH, Serang O, Reinert K, Kohlbacher O.

J Proteome Res. 2020 Feb 13. doi: 10.1021/acs.jproteome.9b00566. [Epub ahead of print]

PMID:
31975601
2.

Alphabet Projection of Spectra.

Kreitzberg PA, Bern M, Shu Q, Yang F, Serang O.

J Proteome Res. 2019 Sep 6;18(9):3268-3281. doi: 10.1021/acs.jproteome.9b00216. Epub 2019 Jul 29.

PMID:
31318211
3.

Yeast membrane proteomics using leucine metabolic labelling: Bioinformatic data processing and exemplary application to the ER-intramembrane protease Ypf1.

Nilse L, Avci D, Heisterkamp P, Serang O, Lemberg MK, Schilling O.

Biochim Biophys Acta. 2016 Oct;1864(10):1363-71. doi: 10.1016/j.bbapap.2016.07.002. Epub 2016 Jul 15.

PMID:
27426920
4.

A research roadmap for next-generation sequencing informatics.

Altman RB, Prabhu S, Sidow A, Zook JM, Goldfeder R, Litwack D, Ashley E, Asimenos G, Bustamante CD, Donigan K, Giacomini KM, Johansen E, Khuri N, Lee E, Liang XS, Salit M, Serang O, Tezak Z, Wall DP, Mansfield E, Kass-Hout T.

Sci Transl Med. 2016 Apr 20;8(335):335ps10. doi: 10.1126/scitranslmed.aaf7314. Review.

5.

Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less.

Serang O, Käll L.

J Proteome Res. 2015 Oct 2;14(10):4099-103. doi: 10.1021/acs.jproteome.5b00568. Epub 2015 Aug 28.

PMID:
26257019
6.

A Fast Numerical Method for Max-Convolution and the Application to Efficient Max-Product Inference in Bayesian Networks.

Serang O.

J Comput Biol. 2015 Aug;22(8):770-83. doi: 10.1089/cmb.2015.0013. Epub 2015 Jul 10.

PMID:
26161499
7.

Quantitative SNP genotyping of polyploids with MassARRAY and other platforms.

Mollinari M, Serang O.

Methods Mol Biol. 2015;1245:215-41. doi: 10.1007/978-1-4939-1966-6_17.

PMID:
25373761
8.

The probabilistic convolution tree: efficient exact Bayesian inference for faster LC-MS/MS protein inference.

Serang O.

PLoS One. 2014 Mar 13;9(3):e91507. doi: 10.1371/journal.pone.0091507. eCollection 2014.

9.

SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids.

Garcia AA, Mollinari M, Marconi TG, Serang OR, Silva RR, Vieira ML, Vicentini R, Costa EA, Mancini MC, Garcia MO, Pastina MM, Gazaffi R, Martins ER, Dahmer N, Sforça DA, Silva CB, Bundock P, Henry RJ, Souza GM, van Sluys MA, Landell MG, Carneiro MS, Vincentz MA, Pinto LR, Vencovsky R, Souza AP.

Sci Rep. 2013 Dec 2;3:3399. doi: 10.1038/srep03399.

10.

Nonparametric Bayesian evaluation of differential protein quantification.

Serang O, Cansizoglu AE, Käll L, Steen H, Steen JA.

J Proteome Res. 2013 Oct 4;12(10):4556-65. doi: 10.1021/pr400678m. Epub 2013 Sep 11.

11.

SweetSEQer, simple de novo filtering and annotation of glycoconjugate mass spectra.

Serang O, Froehlich JW, Muntel J, McDowell G, Steen H, Lee RS, Steen JA.

Mol Cell Proteomics. 2013 Jun;12(6):1735-40. doi: 10.1074/mcp.O112.025940. Epub 2013 Feb 26.

12.

A classifier based on accurate mass measurements to aid large scale, unbiased glycoproteomics.

Froehlich JW, Dodds ED, Wilhelm M, Serang O, Steen JA, Lee RS.

Mol Cell Proteomics. 2013 Apr;12(4):1017-25. doi: 10.1074/mcp.M112.025494. Epub 2013 Feb 25.

13.

A non-parametric cutout index for robust evaluation of identified proteins.

Serang O, Paulo J, Steen H, Steen JA.

Mol Cell Proteomics. 2013 Mar;12(3):807-12. doi: 10.1074/mcp.O112.022863. Epub 2013 Jan 4.

14.

Concerning the accuracy of Fido and parameter choice.

Serang O.

Bioinformatics. 2013 Feb 1;29(3):412. doi: 10.1093/bioinformatics/bts687. Epub 2012 Nov 28. No abstract available.

15.

Recognizing uncertainty increases robustness and reproducibility of mass spectrometry-based protein inferences.

Serang O, Moruz L, Hoopmann MR, Käll L.

J Proteome Res. 2012 Dec 7;11(12):5586-91. doi: 10.1021/pr300426s. Epub 2012 Nov 19.

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18.

Efficient exact maximum a posteriori computation for bayesian SNP genotyping in polyploids.

Serang O, Mollinari M, Garcia AA.

PLoS One. 2012;7(2):e30906. doi: 10.1371/journal.pone.0030906. Epub 2012 Feb 17.

19.

Faster mass spectrometry-based protein inference: junction trees are more efficient than sampling and marginalization by enumeration.

Serang O, Noble WS.

IEEE/ACM Trans Comput Biol Bioinform. 2012 May-Jun;9(3):809-17. doi: 10.1109/TCBB.2012.26.

20.

Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data.

Serang O, MacCoss MJ, Noble WS.

J Proteome Res. 2010 Oct 1;9(10):5346-57. doi: 10.1021/pr100594k.

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