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Items: 12

1.

QuaPra: Efficient transcript assembly and quantification using quadratic programming with Apriori algorithm.

Ji X, Tong W, Ning B, Mason CE, Kreil DP, Labaj PP, Chen G, Shi T.

Sci China Life Sci. 2019 Jul;62(7):937-946. doi: 10.1007/s11427-018-9433-3. Epub 2019 May 22.

PMID:
31124003
2.

The Gpr1-regulated Sur7 family protein Sfp2 is required for hyphal growth and cell wall stability in the mycoparasite Trichoderma atroviride.

Atanasova L, Gruber S, Lichius A, Radebner T, Abendstein L, Münsterkötter M, Stralis-Pavese N, Łabaj PP, Kreil DP, Zeilinger S.

Sci Rep. 2018 Aug 13;8(1):12064. doi: 10.1038/s41598-018-30500-y.

3.
4.

Microarray profiling of preselected CHO host cell subclones identifies gene expression patterns associated with increased production capacity.

Harreither E, Hackl M, Pichler J, Shridhar S, Auer N, Łabaj PP, Scheideler M, Karbiener M, Grillari J, Kreil DP, Borth N.

Biotechnol J. 2015 Oct;10(10):1625-38. doi: 10.1002/biot.201400857. Epub 2015 Sep 23.

PMID:
26315449
5.

Experiences with workflows for automating data-intensive bioinformatics.

Spjuth O, Bongcam-Rudloff E, Hernández GC, Forer L, Giovacchini M, Guimera RV, Kallio A, Korpelainen E, Kańduła MM, Krachunov M, Kreil DP, Kulev O, Łabaj PP, Lampa S, Pireddu L, Schönherr S, Siretskiy A, Vassilev D.

Biol Direct. 2015 Aug 19;10:43. doi: 10.1186/s13062-015-0071-8.

6.

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures.

Munro SA, Lund SP, Pine PS, Binder H, Clevert DA, Conesa A, Dopazo J, Fasold M, Hochreiter S, Hong H, Jafari N, Kreil DP, Łabaj PP, Li S, Liao Y, Lin SM, Meehan J, Mason CE, Santoyo-Lopez J, Setterquist RA, Shi L, Shi W, Smyth GK, Stralis-Pavese N, Su Z, Tong W, Wang C, Wang J, Xu J, Ye Z, Yang Y, Yu Y, Salit M.

Nat Commun. 2014 Sep 25;5:5125. doi: 10.1038/ncomms6125.

PMID:
25254650
7.

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.

Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, Fang H, Hong H, Shen J, Su Z, Meehan J, Li X, Yang L, Li H, Łabaj PP, Kreil DP, Megherbi D, Gaj S, Caiment F, van Delft J, Kleinjans J, Scherer A, Devanarayan V, Wang J, Yang Y, Qian HR, Lancashire LJ, Bessarabova M, Nikolsky Y, Furlanello C, Chierici M, Albanese D, Jurman G, Riccadonna S, Filosi M, Visintainer R, Zhang KK, Li J, Hsieh JH, Svoboda DL, Fuscoe JC, Deng Y, Shi L, Paules RS, Auerbach SS, Tong W.

Nat Biotechnol. 2014 Sep;32(9):926-32. doi: 10.1038/nbt.3001. Epub 2014 Aug 24.

8.

Detecting and correcting systematic variation in large-scale RNA sequencing data.

Li S, Łabaj PP, Zumbo P, Sykacek P, Shi W, Shi L, Phan J, Wu PY, Wang M, Wang C, Thierry-Mieg D, Thierry-Mieg J, Kreil DP, Mason CE.

Nat Biotechnol. 2014 Sep;32(9):888-95. doi: 10.1038/nbt.3000. Epub 2014 Aug 24.

9.

Improving RNA-Seq Precision with MapAl.

Labaj PP, Linggi BE, Wiley HS, Kreil DP.

Front Genet. 2012 Apr 2;3:28. doi: 10.3389/fgene.2012.00028. eCollection 2012.

10.

Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.

Łabaj PP, Leparc GG, Linggi BE, Markillie LM, Wiley HS, Kreil DP.

Bioinformatics. 2011 Jul 1;27(13):i383-91. doi: 10.1093/bioinformatics/btr247.

11.

An analysis of single amino acid repeats as use case for application specific background models.

Łabaj PP, Sykacek P, Kreil DP.

BMC Bioinformatics. 2011 May 19;12:173. doi: 10.1186/1471-2105-12-173.

12.

Single amino acid repeats in signal peptides.

Labaj PP, Leparc GG, Bardet AF, Kreil G, Kreil DP.

FEBS J. 2010 Aug;277(15):3147-57. doi: 10.1111/j.1742-4658.2010.07720.x. Epub 2010 Jun 17.

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