Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 41

1.

Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data.

Peng X, Pipes L, Xiong H, Green RR, Jones DC, Ruzzo WL, Schroth GP, Mason CE, Palermo RE, Katze MG.

J Med Primatol. 2014 May 8. doi: 10.1111/jmp.12125. [Epub ahead of print]

PMID:
24810475
[PubMed - as supplied by publisher]
2.

De novo discovery of structured ncRNA motifs in genomic sequences.

Ruzzo WL, Gorodkin J.

Methods Mol Biol. 2014;1097:303-18. doi: 10.1007/978-1-62703-709-9_15.

PMID:
24639166
[PubMed - in process]
3.

Concepts and introduction to RNA bioinformatics.

Gorodkin J, Hofacker IL, Ruzzo WL.

Methods Mol Biol. 2014;1097:1-31. doi: 10.1007/978-1-62703-709-9_1.

PMID:
24639152
[PubMed - in process]
4.

Discriminative motif analysis of high-throughput dataset.

Yao Z, Macquarrie KL, Fong AP, Tapscott SJ, Ruzzo WL, Gentleman RC.

Bioinformatics. 2014 Mar 15;30(6):775-83. doi: 10.1093/bioinformatics/btt615. Epub 2013 Oct 25.

PMID:
24162561
[PubMed - indexed for MEDLINE]
5.

A microbial profiling method for the human microbiota using high-throughput sequencing.

Tseng HH, Hullar MA, Li F, Lampe JW, Sandstrom R, Johnson AK, Strate LL, Ruzzo WL, Stamatoyannopoulos J.

Metagenomics (Cairo). 2013;2:235646.

PMID:
24013439
[PubMed]
Free PMC Article
6.

Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.

Yao Z, Fong AP, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ.

Skelet Muscle. 2013 Apr 8;3(1):8. doi: 10.1186/2044-5040-3-8.

PMID:
23566431
[PubMed]
Free PMC Article
7.

Compression of next-generation sequencing reads aided by highly efficient de novo assembly.

Jones DC, Ruzzo WL, Peng X, Katze MG.

Nucleic Acids Res. 2012 Dec;40(22):e171. doi: 10.1093/nar/gks754. Epub 2012 Aug 16.

PMID:
22904078
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Integration of 198 ChIP-seq datasets reveals human cis-regulatory regions.

Bolouri H, Ruzzo WL.

J Comput Biol. 2012 Sep;19(9):989-97. doi: 10.1089/cmb.2012.0100. Epub 2012 Aug 16.

PMID:
22897152
[PubMed - indexed for MEDLINE]
9.

Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain.

Seemann SE, Sunkin SM, Hawrylycz MJ, Ruzzo WL, Gorodkin J.

BMC Genomics. 2012 May 31;13:214. doi: 10.1186/1471-2164-13-214.

PMID:
22651826
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Genetic and epigenetic determinants of neurogenesis and myogenesis.

Fong AP, Yao Z, Zhong JW, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ.

Dev Cell. 2012 Apr 17;22(4):721-35. doi: 10.1016/j.devcel.2012.01.015. Epub 2012 Mar 22.

PMID:
22445365
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

A new approach to bias correction in RNA-Seq.

Jones DC, Ruzzo WL, Peng X, Katze MG.

Bioinformatics. 2012 Apr 1;28(7):921-8. doi: 10.1093/bioinformatics/bts055. Epub 2012 Jan 28.

PMID:
22285831
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy.

Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R, Tapscott SJ.

Dev Cell. 2012 Jan 17;22(1):38-51. doi: 10.1016/j.devcel.2011.11.013. Epub 2011 Dec 29.

PMID:
22209328
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription.

Knouf EC, Garg K, Arroyo JD, Correa Y, Sarkar D, Parkin RK, Wurz K, O'Briant KC, Godwin AK, Urban ND, Ruzzo WL, Gentleman R, Drescher CW, Swisher EM, Tewari M.

Nucleic Acids Res. 2012 Jan;40(2):499-510. doi: 10.1093/nar/gkr731. Epub 2011 Sep 14.

PMID:
21917857
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL, Gentleman RC, Tapscott SJ.

Dev Cell. 2010 Apr 20;18(4):662-74. doi: 10.1016/j.devcel.2010.02.014.

PMID:
20412780
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

De novo prediction of structured RNAs from genomic sequences.

Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL.

Trends Biotechnol. 2010 Jan;28(1):9-19. doi: 10.1016/j.tibtech.2009.09.006. Epub 2009 Nov 26. Review.

PMID:
19942311
[PubMed - indexed for MEDLINE]
16.

Finding non-coding RNAs through genome-scale clustering.

Tseng HH, Weinberg Z, Gore J, Breaker RR, Ruzzo WL.

J Bioinform Comput Biol. 2009 Apr;7(2):373-88.

PMID:
19340921
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.

Anandam P, Torarinsson E, Ruzzo WL.

Bioinformatics. 2009 Mar 1;25(5):668-9. doi: 10.1093/bioinformatics/btp006. Epub 2009 Jan 9.

PMID:
19136551
[PubMed - indexed for MEDLINE]
Free Article
18.

MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.

Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R, Ruohola-Baker H, Tewari M.

Stem Cells. 2008 Oct;26(10):2496-505. doi: 10.1634/stemcells.2008-0356. Epub 2008 Jun 26.

PMID:
18583537
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.

Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR.

RNA. 2008 May;14(5):822-8. doi: 10.1261/rna.988608. Epub 2008 Mar 27.

PMID:
18369181
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.

Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR.

Mol Microbiol. 2008 May;68(4):918-32. doi: 10.1111/j.1365-2958.2008.06208.x. Epub 2008 Mar 19.

PMID:
18363797
[PubMed - indexed for MEDLINE]
Free PMC Article

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Loading ...
Write to the Help Desk