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Items: 22

1.

Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects.

Tiuryn J, Szczurek E.

Bioinformatics. 2019 Jul 15;35(14):i605-i614. doi: 10.1093/bioinformatics/btz334.

2.

Correction: Epistasis in genomic and survival data of cancer patients.

Matlak D, Szczurek E.

PLoS Comput Biol. 2019 Feb 27;15(2):e1006887. doi: 10.1371/journal.pcbi.1006887. eCollection 2019 Feb.

3.

Predicting cancer type from tumour DNA signatures.

Soh KP, Szczurek E, Sakoparnig T, Beerenwinkel N.

Genome Med. 2017 Nov 28;9(1):104. doi: 10.1186/s13073-017-0493-2.

4.

Epistasis in genomic and survival data of cancer patients.

Matlak D, Szczurek E.

PLoS Comput Biol. 2017 Jul 5;13(7):e1005626. doi: 10.1371/journal.pcbi.1005626. eCollection 2017 Jul. Erratum in: PLoS Comput Biol. 2019 Feb 27;15(2):e1006887.

5.

Linear effects models of signaling pathways from combinatorial perturbation data.

Szczurek E, Beerenwinkel N.

Bioinformatics. 2016 Jun 15;32(12):i297-i305. doi: 10.1093/bioinformatics/btw268.

6.

Erratum to: gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens.

Schmich F, Szczurek E, Kreibich S, Dilling S, Andritschke D, Casanova A, Low SH, Eicher S, Muntwiler S, Emmenlauer M, Rämo P, Conde-Alvarez R, von Mering C, Hardt WD, Dehio C, Beerenwinkel N.

Genome Biol. 2015 Oct 21;16:233. doi: 10.1186/s13059-015-0807-x. No abstract available.

7.

gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens.

Schmich F, Szczurek E, Kreibich S, Dilling S, Andritschke D, Casanova A, Low SH, Eicher S, Muntwiler S, Emmenlauer M, Rämö P, Conde-Alvarez R, von Mering C, Hardt WD, Dehio C, Beerenwinkel N.

Genome Biol. 2015 Oct 7;16:220. doi: 10.1186/s13059-015-0783-1. Erratum in: Genome Biol. 2015;16:233.

8.

TiMEx: a waiting time model for mutually exclusive cancer alterations.

Constantinescu S, Szczurek E, Mohammadi P, Rahnenführer J, Beerenwinkel N.

Bioinformatics. 2016 Apr 1;32(7):968-75. doi: 10.1093/bioinformatics/btv400. Epub 2015 Jul 9.

PMID:
26163509
9.

Simultaneous analysis of large-scale RNAi screens for pathogen entry.

Rämö P, Drewek A, Arrieumerlou C, Beerenwinkel N, Ben-Tekaya H, Cardel B, Casanova A, Conde-Alvarez R, Cossart P, Csúcs G, Eicher S, Emmenlauer M, Greber U, Hardt WD, Helenius A, Kasper C, Kaufmann A, Kreibich S, Kühbacher A, Kunszt P, Low SH, Mercer J, Mudrak D, Muntwiler S, Pelkmans L, Pizarro-Cerdá J, Podvinec M, Pujadas E, Rinn B, Rouilly V, Schmich F, Siebourg-Polster J, Snijder B, Stebler M, Studer G, Szczurek E, Truttmann M, von Mering C, Vonderheit A, Yakimovich A, Bühlmann P, Dehio C.

BMC Genomics. 2014 Dec 22;15:1162. doi: 10.1186/1471-2164-15-1162.

10.

Inferring the paths of somatic evolution in cancer.

Misra N, Szczurek E, Vingron M.

Bioinformatics. 2014 Sep 1;30(17):2456-63. doi: 10.1093/bioinformatics/btu319. Epub 2014 May 7.

PMID:
24812340
11.

Modeling mutual exclusivity of cancer mutations.

Szczurek E, Beerenwinkel N.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003503. doi: 10.1371/journal.pcbi.1003503. eCollection 2014 Mar.

12.

(-)-R-mevalonolactone studied by ROA and SERS spectroscopy.

Chruszcz-Lipska K, Jaworska A, Szczurek E, Baranska M.

Chirality. 2014 Sep;26(9):453-61. doi: 10.1002/chir.22288. Epub 2014 Jan 16.

PMID:
24431105
13.

Synthetic sickness or lethality points at candidate combination therapy targets in glioblastoma.

Szczurek E, Misra N, Vingron M.

Int J Cancer. 2013 Nov;133(9):2123-32. doi: 10.1002/ijc.28235. Epub 2013 Jun 4.

14.

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers.

Jankowski A, Szczurek E, Jauch R, Tiuryn J, Prabhakar S.

Genome Res. 2013 Aug;23(8):1307-18. doi: 10.1101/gr.154922.113. Epub 2013 Apr 3.

15.

Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.

Szczurek E, Markowetz F, Gat-Viks I, Biecek P, Tiuryn J, Vingron M.

BMC Bioinformatics. 2011 Jun 21;12:249. doi: 10.1186/1471-2105-12-249.

16.

Introducing knowledge into differential expression analysis.

Szczurek E, Biecek P, Tiuryn J, Vingron M.

J Comput Biol. 2010 Aug;17(8):953-67. doi: 10.1089/cmb.2010.0034.

17.

On subset seeds for protein alignment.

Roytberg M, Gambin A, Noé L, Lasota S, Furletova E, Szczurek E, Kucherov G.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Jul-Sep;6(3):483-94. doi: 10.1109/TCBB.2009.4.

PMID:
19644175
18.

Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments.

Szczurek E, Gat-Viks I, Tiuryn J, Vingron M.

Mol Syst Biol. 2009;5:287. doi: 10.1038/msb.2009.45. Epub 2009 Jul 7.

19.

Renal metallothionein responds rapidly and site specifically to zinc repletion in growing rats.

Szczurek EI, Bjornsson CS, Noto AD, Taylor CG.

J Trace Elem Med Biol. 2009;23(3):176-82. doi: 10.1016/j.jtemb.2009.03.005. Epub 2009 May 8.

PMID:
19486827
20.

Classification of peptide mass fingerprint data by novel no-regret boosting method.

Gambin A, Szczurek E, Dutkowski J, Bakun M, Dadlez M.

Comput Biol Med. 2009 May;39(5):460-73. doi: 10.1016/j.compbiomed.2009.03.006. Epub 2009 Apr 21.

PMID:
19386298
21.

Putative type IV secretion genes in Bacillus anthracis.

Grynberg M, Li Z, Szczurek E, Godzik A.

Trends Microbiol. 2007 May;15(5):191-5. Epub 2007 Mar 26.

PMID:
17387016
22.

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