Walter L Ruzzo

Walter L Ruzzo

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Walter L Ruzzo

Walter L Ruzzo

Publications by authors named "Walter L Ruzzo"

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Identification and characterization of novel conserved RNA structures in Drosophila.

BMC Genomics 2018 Dec 11;19(1):899. Epub 2018 Dec 11.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, Frederiksberg C, DK-1870, Denmark.

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http://dx.doi.org/10.1186/s12864-018-5234-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6288889PMC
December 2018

Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis.

Cell Rep 2017 08;20(7):1597-1608

Department of Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Medicine/Cardiology, University of Washington School of Medicine, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.07.067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5576510PMC
August 2017

Associating transcription factors and conserved RNA structures with gene regulation in the human brain.

Sci Rep 2017 07 18;7(1):5776. Epub 2017 Jul 18.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870, Frederiksberg C, Denmark.

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http://dx.doi.org/10.1038/s41598-017-06200-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5516038PMC
July 2017

Inhibition of β-catenin signaling respecifies anterior-like endothelium into beating human cardiomyocytes.

Development 2015 Sep 7;142(18):3198-209. Epub 2015 Jul 7.

Department of Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA Center for Cardiovascular Biology, University of Washington School of Medicine, Seattle, WA 98109, USA Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA Department of Bioengineering, University of Washington School of Medicine, Seattle, WA 98109, USA Department of Medicine/Cardiology, University of Washington School of Medicine, Seattle, WA 98109, USA

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http://dev.biologists.org/cgi/doi/10.1242/dev.117010
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http://dx.doi.org/10.1242/dev.117010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4582173PMC
September 2015

Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes.

Proc Natl Acad Sci U S A 2015 May 11;112(21):E2785-94. Epub 2015 May 11.

Institute for Stem Cell and Regenerative Medicine, Seattle, WA 98109; Departments of Biochemistry, Department of Bioengineering, and Department of Genome Sciences, University of Washington, Seattle, WA 98195; Department of Biology, University of Washington, Seattle, WA 98195

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http://www.pnas.org/lookup/doi/10.1073/pnas.1424042112
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http://dx.doi.org/10.1073/pnas.1424042112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450404PMC
May 2015

Concepts and introduction to RNA bioinformatics.

Methods Mol Biol 2014 ;1097:1-31

Center for non-coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg C, Denmark.

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http://dx.doi.org/10.1007/978-1-62703-709-9_1DOI Listing
November 2014

De novo discovery of structured ncRNA motifs in genomic sequences.

Methods Mol Biol 2014 ;1097:303-18

Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.

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http://dx.doi.org/10.1007/978-1-62703-709-9_15DOI Listing
November 2014

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

J Med Primatol 2014 Oct 8;43(5):317-28. Epub 2014 May 8.

Department of Microbiology, University of Washington, Seattle, WA, USA; Washington National Primate Research Center, Seattle, WA, USA.

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http://dx.doi.org/10.1111/jmp.12125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176519PMC
October 2014

Discriminative motif analysis of high-throughput dataset.

Bioinformatics 2014 Mar 25;30(6):775-83. Epub 2013 Oct 25.

Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, 98105, USA, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Department of Pediatrics, School of Medicine, Department of Neurology, School of Medicine, University of Washington, Seattle, Washington, 98105, USA, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Department of Computer Science and Engineering, Department of Genome Sciences, University of Washington, Seattle, Washington, 98105, USA and Bioinformatics and Computational Biology, Genentech, South San Francisco, CA 94080, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3957073PMC
March 2014

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

Nucleic Acids Res 2012 Dec 16;40(22):e171. Epub 2012 Aug 16.

Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA.

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https://academic.oup.com/nar/article/40/22/e171/1137542
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http://dx.doi.org/10.1093/nar/gks754DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526293PMC
December 2012

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

J Comput Biol 2012 Sep 16;19(9):989-97. Epub 2012 Aug 16.

Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1089/cmb.2012.0100DOI Listing
September 2012

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

BMC Genomics 2012 May 31;13:214. Epub 2012 May 31.

Center for non-coding RNA in Technology and Health, University of Copenhagen, Denmark.

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http://dx.doi.org/10.1186/1471-2164-13-214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3464589PMC
May 2012

A new approach to bias correction in RNA-Seq.

Bioinformatics 2012 Apr 28;28(7):921-8. Epub 2012 Jan 28.

Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315719PMC
April 2012

Genetic and epigenetic determinants of neurogenesis and myogenesis.

Dev Cell 2012 Apr 22;22(4):721-35. Epub 2012 Mar 22.

Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1016/j.devcel.2012.01.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3331915PMC
April 2012

De novo prediction of structured RNAs from genomic sequences.

Trends Biotechnol 2010 Jan 26;28(1):9-19. Epub 2009 Nov 26.

Section for Genetics and Bioinformatics, IBHV and Center for Applied Bioinformatics, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1016/j.tibtech.2009.09.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4712260PMC
January 2010

Finding non-coding RNAs through genome-scale clustering.

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

Department of Computer Science & Engineering, University of Washington, Seattle, WA 98195-2350, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3417115PMC
April 2009

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

Bioinformatics 2009 Mar 9;25(5):668-9. Epub 2009 Jan 9.

Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp006DOI Listing
March 2009

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

RNA 2008 May 27;14(5):822-8. Epub 2008 Mar 27.

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.

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http://www.rnajournal.org/cgi/doi/10.1261/rna.988608
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http://dx.doi.org/10.1261/rna.988608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2327355PMC
May 2008

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.

Genome Res 2008 Feb 20;18(2):242-51. Epub 2007 Dec 20.

Section for Genetics and Bioinformatics, IBVH, Faculty of Life Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1101/gr.6887408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2203622PMC
February 2008

How accurately is ncRNA aligned within whole-genome multiple alignments?

BMC Bioinformatics 2007 Oct 26;8:417. Epub 2007 Oct 26.

Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/1471-2105-8-417DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206062PMC
October 2007

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.

Nucleic Acids Res 2007 9;35(14):4809-19. Epub 2007 Jul 9.

Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103, USA.

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http://dx.doi.org/10.1093/nar/gkm487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950547PMC
September 2007

A Marfan syndrome gene expression phenotype in cultured skin fibroblasts.

BMC Genomics 2007 Sep 12;8:319. Epub 2007 Sep 12.

Department of Pathology, University of Washington, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1186/1471-2164-8-319DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2174953PMC
September 2007

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.

PLoS Comput Biol 2007 Jul;3(7):e126

Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1371/journal.pcbi.0030126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1913097PMC
July 2007

A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data.

BMC Bioinformatics 2006 Mar 20;7 Suppl 1:S11. Epub 2006 Mar 20.

Department of Computer Science and Engineering, AC101 Paul G. Allen Center, University of Washington, Seattle WA 98195, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-7-S1-S11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810312PMC
March 2006

CMfinder--a covariance model based RNA motif finding algorithm.

Bioinformatics 2006 Feb 15;22(4):445-52. Epub 2005 Dec 15.

Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA.

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http://dx.doi.org/10.1093/bioinformatics/btk008DOI Listing
February 2006

Sequence-based heuristics for faster annotation of non-coding RNA families.

Bioinformatics 2006 Jan 2;22(1):35-9. Epub 2005 Nov 2.

Department of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti743DOI Listing
January 2006

6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.

RNA 2005 May 5;11(5):774-84. Epub 2005 Apr 5.

Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1261/rna.7286705DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1370762PMC
May 2005

A glycine-dependent riboswitch that uses cooperative binding to control gene expression.

Science 2004 Oct;306(5694):275-9

Department of Molecular, Cellular, and Developmental Biology, Yale University, Post Office Box 208103, New Haven, CT 06520-8103, USA.

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http://dx.doi.org/10.1126/science.1100829DOI Listing
October 2004

Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy.

Bioinformatics 2004 Aug;20 Suppl 1:i334-41

Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth925DOI Listing
August 2004

Atherosclerotic plaque smooth muscle cells have a distinct phenotype.

Arterioscler Thromb Vasc Biol 2004 Jul 13;24(7):1283-9. Epub 2004 May 13.

Department of Pathology, University of Washington, Box 357335, Seattle, Wash 98195-7335, USA.

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http://dx.doi.org/10.1161/01.ATV.0000132401.12275.0cDOI Listing
July 2004

Pre-mRNA secondary structure prediction aids splice site prediction.

Pac Symp Biocomput 2002 :223-34

University of Washington, Box 352350, Seattle, WA 98195, USA.

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October 2002