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Items: 1 to 50 of 97

1.

In Vivo Chemical Probing for G-Quadruplex Formation.

Kouzine F, Wojtowicz D, Yamane A, Casellas R, Przytycka TM, Levens DL.

Methods Mol Biol. 2019;2035:369-382. doi: 10.1007/978-1-4939-9666-7_23.

PMID:
31444763
2.

Author Correction: Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila.

Wang Y, Cho DY, Lee H, Fear J, Oliver B, Przytycka TM.

Nat Commun. 2019 Jul 29;10(1):3458. doi: 10.1038/s41467-019-11418-z.

3.

Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer.

Wojtowicz D, Sason I, Huang X, Kim YA, Leiserson MDM, Przytycka TM, Sharan R.

Genome Med. 2019 Jul 26;11(1):49. doi: 10.1186/s13073-019-0659-1.

4.

Subpopulation Detection and Their Comparative Analysis across Single-Cell Experiments with scPopCorn.

Wang Y, Hoinka J, Przytycka TM.

Cell Syst. 2019 Jun 26;8(6):506-513.e5. doi: 10.1016/j.cels.2019.05.007. Epub 2019 Jun 19.

5.

Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro.

Pal S, Hoinka J, Przytycka TM.

Nucleic Acids Res. 2019 Jul 26;47(13):6632-6641. doi: 10.1093/nar/gkz540.

6.

Correction to: 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. 2019 Mar 11;20(1):53. doi: 10.1186/s13059-019-1668-5.

7.

Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila.

Wang Y, Cho DY, Lee H, Fear J, Oliver B, Przytycka TM.

Nat Commun. 2018 Oct 3;9(1):4061. doi: 10.1038/s41467-018-06382-z. Erratum in: Nat Commun. 2019 Jul 29;10(1):3458.

8.

From hype to reality: data science enabling personalized medicine.

Fröhlich H, Balling R, Beerenwinkel N, Kohlbacher O, Kumar S, Lengauer T, Maathuis MH, Moreau Y, Murphy SA, Przytycka TM, Rebhan M, Röst H, Schuppert A, Schwab M, Spang R, Stekhoven D, Sun J, Weber A, Ziemek D, Zupan B.

BMC Med. 2018 Aug 27;16(1):150. doi: 10.1186/s12916-018-1122-7.

9.

A 2'FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein.

Shubham S, Hoinka J, Banerjee S, Swanson E, Dillard JA, Lennemann NJ, Przytycka TM, Maury W, Nilsen-Hamilton M.

Sci Rep. 2018 Aug 17;8(1):12373. doi: 10.1038/s41598-018-30590-8.

10.

AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems.

Wang Y, Hoinka J, Liang Y, Adamus T, Swiderski P, Przytycka TM.

Nucleic Acids Res. 2018 Sep 19;46(16):8133-8142. doi: 10.1093/nar/gky577.

11.

AptaSUITE: A Full-Featured Bioinformatics Framework for the Comprehensive Analysis of Aptamers from HT-SELEX Experiments.

Hoinka J, Backofen R, Przytycka TM.

Mol Ther Nucleic Acids. 2018 Jun 1;11:515-517. doi: 10.1016/j.omtn.2018.04.006. Epub 2018 Apr 22. No abstract available.

12.

LDSplitDB: a database for studies of meiotic recombination hotspots in MHC using human genomic data.

Guo J, Chen H, Yang P, Lee YT, Wu M, Przytycka TM, Kwoh CK, Zheng J.

BMC Med Genomics. 2018 Apr 20;11(Suppl 2):27. doi: 10.1186/s12920-018-0351-0.

13.

Dosage-Dependent Expression Variation Suppressed on the Drosophila Male X Chromosome.

Lee H, Cho DY, Wojtowicz D, Harbison ST, Russell S, Oliver B, Przytycka TM.

G3 (Bethesda). 2018 Feb 2;8(2):587-598. doi: 10.1534/g3.117.300400.

14.

Mapping DNA Breaks by Next-Generation Sequencing.

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

Methods Mol Biol. 2018;1672:155-166. doi: 10.1007/978-1-4939-7306-4_13.

PMID:
29043624
15.

Detecting presence of mutational signatures in cancer with confidence.

Huang X, Wojtowicz D, Przytycka TM.

Bioinformatics. 2017 Sep 22. doi: 10.1093/bioinformatics/btx604. [Epub ahead of print]

16.

BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.

Dao P, Kim YA, Wojtowicz D, Madan S, Sharan R, Przytycka TM.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005695. doi: 10.1371/journal.pcbi.1005695. eCollection 2017 Oct.

17.

Aptamer-Drug Conjugates of Active Metabolites of Nucleoside Analogs and Cytotoxic Agents Inhibit Pancreatic Tumor Cell Growth.

Yoon S, Huang KW, Reebye V, Spalding D, Przytycka TM, Wang Y, Swiderski P, Li L, Armstrong B, Reccia I, Zacharoulis D, Dimas K, Kusano T, Shively J, Habib N, Rossi JJ.

Mol Ther Nucleic Acids. 2017 Mar 17;6:80-88. doi: 10.1016/j.omtn.2016.11.008. Epub 2016 Dec 10.

18.

Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome.

Kouzine F, Wojtowicz D, Baranello L, Yamane A, Nelson S, Resch W, Kieffer-Kwon KR, Benham CJ, Casellas R, Przytycka TM, Levens D.

Cell Syst. 2017 Mar 22;4(3):344-356.e7. doi: 10.1016/j.cels.2017.01.013. Epub 2017 Feb 22.

19.

Highly Constrained Bicyclic Scaffolds for the Discovery of Protease-Stable Peptides via mRNA Display.

Hacker DE, Hoinka J, Iqbal ES, Przytycka TM, Hartman MC.

ACS Chem Biol. 2017 Mar 17;12(3):795-804. doi: 10.1021/acschembio.6b01006. Epub 2017 Feb 1.

20.

AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments.

Dao P, Hoinka J, Takahashi M, Zhou J, Ho M, Wang Y, Costa F, Rossi JJ, Backofen R, Burnett J, Przytycka TM.

Cell Syst. 2016 Jul;3(1):62-70. doi: 10.1016/j.cels.2016.07.003.

21.

WeSME: uncovering mutual exclusivity of cancer drivers and beyond.

Kim YA, Madan S, Przytycka TM.

Bioinformatics. 2017 Mar 15;33(6):814-821. doi: 10.1093/bioinformatics/btw242.

22.

Ups and Downs of Poised RNA Polymerase II in B-Cells.

Dao P, Wojtowicz D, Nelson S, Levens D, Przytycka TM.

PLoS Comput Biol. 2016 Apr 14;12(4):e1004821. doi: 10.1371/journal.pcbi.1004821. eCollection 2016 Apr.

23.

Correlated rigid modes in protein families.

Striegel DA, Wojtowicz D, Przytycka TM, Periwal V.

Phys Biol. 2016 Apr 11;13(2):025003. doi: 10.1088/1478-3975/13/2/025003.

24.

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription.

Baranello L, Wojtowicz D, Cui K, Devaiah BN, Chung HJ, Chan-Salis KY, Guha R, Wilson K, Zhang X, Zhang H, Piotrowski J, Thomas CJ, Singer DS, Pugh BF, Pommier Y, Przytycka TM, Kouzine F, Lewis BA, Zhao K, Levens D.

Cell. 2016 Apr 7;165(2):357-71. doi: 10.1016/j.cell.2016.02.036.

25.

Understanding Genotype-Phenotype Effects in Cancer via Network Approaches.

Kim YA, Cho DY, Przytycka TM.

PLoS Comput Biol. 2016 Mar 10;12(3):e1004747. doi: 10.1371/journal.pcbi.1004747. eCollection 2016 Mar. Review.

26.

Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways.

Zhang F, Chen H, Zhao LN, Liu H, Przytycka TM, Zheng J.

BMC Syst Biol. 2016 Jan 11;10 Suppl 1:7. doi: 10.1186/s12918-015-0249-9.

27.

ARG-walker: inference of individual specific strengths of meiotic recombination hotspots by population genomics analysis.

Chen H, Yang P, Guo J, Kwoh CK, Przytycka TM, Zheng J.

BMC Genomics. 2015;16 Suppl 12:S1. doi: 10.1186/1471-2164-16-S12-S1. Epub 2015 Dec 9.

28.

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples.

Jin W, Tang Q, Wan M, Cui K, Zhang Y, Ren G, Ni B, Sklar J, Przytycka TM, Childs R, Levens D, Zhao K.

Nature. 2015 Dec 3;528(7580):142-6. doi: 10.1038/nature15740.

29.

AptaGUI-A Graphical User Interface for the Efficient Analysis of HT-SELEX Data.

Hoinka J, Dao P, Przytycka TM.

Mol Ther Nucleic Acids. 2015 Oct 13;4:e257. doi: 10.1038/mtna.2015.26. No abstract available.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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. Erratum in: Genome Biol. 2019 Mar 11;20(1):53.

38.

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):2031-2043. doi: 10.1016/j.celrep.2014.08.038. Epub 2014 Sep 18.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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

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

Pac Symp Biocomput. 2013:135-46.

50.

Transcription-dependent dynamic supercoiling is a short-range genomic force.

Kouzine F, Gupta A, Baranello L, Wojtowicz D, Ben-Aissa K, Liu J, Przytycka TM, Levens D.

Nat Struct Mol Biol. 2013 Mar;20(3):396-403. doi: 10.1038/nsmb.2517. Epub 2013 Feb 17.

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