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Results: 1 to 20 of 59

1.

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.

PMID:
25056547
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24985915
[PubMed - in process]
Free PMC Article
3.

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.

PMID:
24533858
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
24037092
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
23920358
[PubMed - indexed for MEDLINE]
6.

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.

PMID:
23821670
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23755066
[PubMed]
Free PMC Article
8.

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.

PMID:
23706737
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23620297
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
23424148
[PubMed - indexed for MEDLINE]
Free Article
11.

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

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

Pac Symp Biocomput. 2013:135-46.

PMID:
23424119
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
23416947
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Chapter 5: Network biology approach to complex diseases.

Cho DY, Kim YA, Przytycka TM.

PLoS Comput Biol. 2012;8(12):e1002820. doi: 10.1371/journal.pcbi.1002820. Epub 2012 Dec 27.

PMID:
23300411
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies.

Salari R, Kimchi-Sarfaty C, Gottesman MM, Przytycka TM.

Nucleic Acids Res. 2013 Jan 7;41(1):44-53. doi: 10.1093/nar/gks1009. Epub 2012 Nov 3.

PMID:
23125360
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Teasing apart translational and transcriptional components of stochastic variations in eukaryotic gene expression.

Salari R, Wojtowicz D, Zheng J, Levens D, Pilpel Y, Przytycka TM.

PLoS Comput Biol. 2012;8(8):e1002644. doi: 10.1371/journal.pcbi.1002644. Epub 2012 Aug 30. Erratum in: PLoS Comput Biol. 2012;8(10): doi/10.1371/annotation/4498943d-525d-4ac1-8375-ae78e67ea0c8.

PMID:
22956896
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Characterization of coding synonymous and non-synonymous variants in ADAMTS13 using ex vivo and in silico approaches.

Edwards NC, Hing ZA, Perry A, Blaisdell A, Kopelman DB, Fathke R, Plum W, Newell J, Allen CE, S G, Shapiro A, Okunji C, Kosti I, Shomron N, Grigoryan V, Przytycka TM, Sauna ZE, Salari R, Mandel-Gutfreund Y, Komar AA, Kimchi-Sarfaty C.

PLoS One. 2012;7(6):e38864. doi: 10.1371/journal.pone.0038864. Epub 2012 Jun 29.

PMID:
22768050
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Epigenetic functions enriched in transcription factors binding to mouse recombination hotspots.

Wu M, Kwoh CK, Przytycka TM, Li J, Zheng J.

Proteome Sci. 2012 Jun 21;10 Suppl 1:S11. doi: 10.1186/1477-5956-10-S1-S11.

PMID:
22759569
[PubMed]
Free PMC Article
18.

Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers.

Hoinka J, Zotenko E, Friedman A, Sauna ZE, Przytycka TM.

Bioinformatics. 2012 Jun 15;28(12):i215-23. doi: 10.1093/bioinformatics/bts210.

PMID:
22689764
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Crystal structures of the outer membrane domain of intimin and invasin from enterohemorrhagic E. coli and enteropathogenic Y. pseudotuberculosis.

Fairman JW, Dautin N, Wojtowicz D, Liu W, Noinaj N, Barnard TJ, Udho E, Przytycka TM, Cherezov V, Buchanan SK.

Structure. 2012 Jul 3;20(7):1233-43. doi: 10.1016/j.str.2012.04.011. Epub 2012 May 31.

PMID:
22658748
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Analysis of F9 point mutations and their correlation to severity of haemophilia B disease.

Hamasaki-Katagiri N, Salari R, Simhadri VL, Tseng SC, Needlman E, Edwards NC, Sauna ZE, Grigoryan V, Komar AA, Przytycka TM, Kimchi-Sarfaty C.

Haemophilia. 2012 Nov;18(6):933-40. doi: 10.1111/j.1365-2516.2012.02848.x. Epub 2012 May 29.

PMID:
22639855
[PubMed - indexed for MEDLINE]

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