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Results: 1 to 20 of 68

1.

MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types.

Kim YA, Cho DY, Dao P, Przytycka TM.

Bioinformatics. 2015 Jun 15;31(12):i284-92. doi: 10.1093/bioinformatics/btv247.

PMID:
26072494
2.

Identifying high-affinity aptamer ligands with defined cross-reactivity using high-throughput guided systematic evolution of ligands by exponential enrichment.

Levay A, Brenneman R, Hoinka J, Sant D, Cardone M, Trinchieri G, Przytycka TM, Berezhnoy A.

Nucleic Acids Res. 2015 Jul 13;43(12):e82. doi: 10.1093/nar/gkv534. Epub 2015 May 24.

3.

Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery.

Hoinka J, Berezhnoy A, Dao P, Sauna ZE, Gilboa E, Przytycka TM.

Nucleic Acids Res. 2015 Jul 13;43(12):5699-707. doi: 10.1093/nar/gkv308. Epub 2015 Apr 13.

4.

Shapely DNA attracts the right partner.

Przytycka TM, Levens D.

Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4516-7. doi: 10.1073/pnas.1503951112. Epub 2015 Apr 6. No abstract available.

PMID:
25848058
5.

AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application.

Hoinka J, Berezhnoy A, Sauna ZE, Gilboa E, Przytycka TM.

Res Comput Mol Biol. 2014;8394:115-128.

6.

Sex- and tissue-specific functions of Drosophila doublesex transcription factor target genes.

Clough E, Jimenez E, Kim YA, Whitworth C, Neville MC, Hempel LU, Pavlou HJ, Chen ZX, Sturgill D, Dale RK, Smith HE, Przytycka TM, Goodwin SF, Van Doren M, Oliver B.

Dev Cell. 2014 Dec 22;31(6):761-73. doi: 10.1016/j.devcel.2014.11.021.

PMID:
25535918
7.

Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation.

Du X, Gertz EM, Wojtowicz D, Zhabinskaya D, Levens D, Benham CJ, Schäffer AA, Przytycka TM.

Nucleic Acids Res. 2014 Nov 10;42(20):12367-79. doi: 10.1093/nar/gku921. Epub 2014 Oct 21.

8.

DNA copy number evolution in Drosophila cell lines.

Lee H, McManus CJ, Cho DY, Eaton M, Renda F, Somma MP, Cherbas L, May G, Powell S, Zhang D, Zhan L, Resch A, Andrews J, Celniker SE, Cherbas P, Przytycka TM, Gatti M, Oliver B, Graveley B, MacAlpine D.

Genome Biol. 2014 Aug 28;15(8):R70. doi: 10.1186/gb-2014-15-8-r70.

9.

Transcription factor networks in Drosophila melanogaster.

Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker SE, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S.

Cell Rep. 2014 Sep 25;8(6):2031-43. doi: 10.1016/j.celrep.2014.08.038. Epub 2014 Sep 18.

10.

DNA break mapping reveals topoisomerase II activity genome-wide.

Baranello L, Kouzine F, Wojtowicz D, Cui K, Przytycka TM, Zhao K, Levens D.

Int J Mol Sci. 2014 Jul 23;15(7):13111-22. doi: 10.3390/ijms150713111.

11.

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim YA, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu LL, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu YQ, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S.

Genome Res. 2014 Jul;24(7):1209-23. doi: 10.1101/gr.159384.113.

12.

LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms.

Yang P, Wu M, Guo J, Kwoh CK, Przytycka TM, Zheng J.

BMC Bioinformatics. 2014 Feb 17;15:48. doi: 10.1186/1471-2105-15-48.

13.

Endogenous factor VIII synthesis from the intron 22-inverted F8 locus may modulate the immunogenicity of replacement therapy for hemophilia A.

Pandey GS, Yanover C, Miller-Jenkins LM, Garfield S, Cole SA, Curran JE, Moses EK, Rydz N, Simhadri V, Kimchi-Sarfaty C, Lillicrap D, Viel KR, Przytycka TM, Pierce GF, Howard TE, Sauna ZE; PATH (Personalized Alternative Therapies for Hemophilia) Study Investigators.

Nat Med. 2013 Oct;19(10):1318-24. doi: 10.1038/nm.3270. Epub 2013 Sep 15.

14.

A gene-specific method for predicting hemophilia-causing point mutations.

Hamasaki-Katagiri N, Salari R, Wu A, Qi Y, Schiller T, Filiberto AC, Schisterman EF, Komar AA, Przytycka TM, Kimchi-Sarfaty C.

J Mol Biol. 2013 Nov 1;425(21):4023-33. doi: 10.1016/j.jmb.2013.07.037. Epub 2013 Aug 3.

15.

Dissecting cancer heterogeneity with a probabilistic genotype-phenotype model.

Cho DY, Przytycka TM.

Nucleic Acids Res. 2013 Sep;41(17):8011-20. doi: 10.1093/nar/gkt577. Epub 2013 Jul 2.

16.

eQTL Epistasis - Challenges and Computational Approaches.

Huang Y, Wuchty S, Przytycka TM.

Front Genet. 2013 May 31;4:51. doi: 10.3389/fgene.2013.00051. eCollection 2013.

17.

Global regulation of promoter melting in naive lymphocytes.

Kouzine F, Wojtowicz D, Yamane A, Resch W, Kieffer-Kwon KR, Bandle R, Nelson S, Nakahashi H, Awasthi P, Feigenbaum L, Menoni H, Hoeijmakers J, Vermeulen W, Ge H, Przytycka TM, Levens D, Casellas R.

Cell. 2013 May 23;153(5):988-99. doi: 10.1016/j.cell.2013.04.033.

18.

The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli.

Du X, Wojtowicz D, Bowers AA, Levens D, Benham CJ, Przytycka TM.

Nucleic Acids Res. 2013 Jul;41(12):5965-77. doi: 10.1093/nar/gkt308. Epub 2013 Apr 25.

19.

Modeling cell heterogeneity: from single-cell variations to mixed cells.

Batchelor E, Kann MG, Przytycka TM, Raphael BJ, Wojtowicz D.

Pac Symp Biocomput. 2013:445-50.

20.

Module cover - a new approach to genotype-phenotype studies.

Kim YA, Salari R, Wuchty S, Przytycka TM.

Pac Symp Biocomput. 2013:135-46.

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