Publications by authors named "Walter L Ruzzo"

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Does rapid sequence divergence preclude RNA structure conservation in vertebrates?
Stefan E Seemann, Aashiq H Mirza, Claus H Bang-Berthelsen, Christian Garde, Mikkel Christensen-Dalsgaard, Walter L Ruzzo

Nucleic Acids Res· March 2022

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Polee: RNA-Seq analysis using approximate likelihood.
Daniel C Jones, Walter L Ruzzo

NAR Genom Bioinform· June 2021

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Spatial modeling of prostate cancer metabolic gene expression reveals extensive heterogeneity and selective vulnerabilities.
Yuliang Wang, Shuyi Ma, Walter L Ruzzo

Sci Rep· February 2020

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Metabolic Control over mTOR-Dependent Diapause-like State.
Abdiasis M Hussein, Yuliang Wang, Julie Mathieu, Lilyana Margaretha, Chaozhong Song, Walter L Ruzzo

Dev Cell· January 2020

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Identification and characterization of novel conserved RNA structures in Drosophila.
Rebecca Kirsch, Stefan E Seemann, Walter L Ruzzo, Stephen M Cohen, Peter F Stadler

BMC Genomics· December 2018

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Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana.
Julie A Koester, Chris T Berthiaume, Naozumi Hiranuma, Micaela S Parker, Vaughn Iverson, Walter L Ruzzo

Sci Rep· July 2018

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The identification and functional annotation of RNA structures conserved in vertebrates.
Stefan E Seemann, Aashiq H Mirza, Claus Hansen, Claus H Bang-Berthelsen, Christian Garde, Walter L Ruzzo

Genome Res· August 2017

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Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis.
Nathan J Palpant, Yuliang Wang, Brandon Hadland, Rebecca J Zaunbrecher, Meredith Redd, Walter L Ruzzo

Cell Rep· August 2017

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Associating transcription factors and conserved RNA structures with gene regulation in the human brain.
Nikolai Hecker, Stefan E Seemann, Asli Silahtaroglu, Walter L Ruzzo, Jan Gorodkin

Sci Rep· July 2017

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Inhibition of β-catenin signaling respecifies anterior-like endothelium into beating human cardiomyocytes.
Nathan J Palpant, Lil Pabon, Meredith Roberts, Brandon Hadland, Daniel Jones, Walter L Ruzzo

Development· September 2015

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Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes.
Kavitha T Kuppusamy, Daniel C Jones, Henrik Sperber, Anup Madan, Karin A Fischer, Walter L Ruzzo

Proc Natl Acad Sci U S A· May 2015

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Concepts and introduction to RNA bioinformatics.
Jan Gorodkin, Ivo L Hofacker, Walter L Ruzzo

Methods Mol Biol· November 2014

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De novo discovery of structured ncRNA motifs in genomic sequences.
Walter L Ruzzo, Jan Gorodkin

Methods Mol Biol· November 2014

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Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data.
Xinxia Peng, Lenore Pipes, Hao Xiong, Richard R Green, Daniel C Jones, Walter L Ruzzo

J Med Primatol· October 2014

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Discriminative motif analysis of high-throughput dataset.
Zizhen Yao, Kyle L Macquarrie, Abraham P Fong, Stephen J Tapscott, Walter L Ruzzo

Bioinformatics· March 2014

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Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.
Zizhen Yao, Abraham P Fong, Yi Cao, Walter L Ruzzo, Robert C Gentleman

Skelet Muscle· April 2013

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A microbial profiling method for the human microbiota using high-throughput sequencing.
Huei-Hun Elizabeth Tseng, Meredith A J Hullar, Fei Li, Johanna W Lampe, Richard Sandstrom, Walter L Ruzzo

Metagenomics (Cairo)· January 2013

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Compression of next-generation sequencing reads aided by highly efficient de novo assembly.
Daniel C Jones, Walter L Ruzzo, Xinxia Peng, Michael G Katze

Nucleic Acids Res· December 2012

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Integration of 198 ChIP-seq datasets reveals human cis-regulatory regions.
Hamid Bolouri, Walter L Ruzzo

J Comput Biol· September 2012

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Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain.
Stefan E Seemann, Susan M Sunkin, Michael J Hawrylycz, Walter L Ruzzo, Jan Gorodkin

BMC Genomics· May 2012

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A new approach to bias correction in RNA-Seq.
Daniel C Jones, Walter L Ruzzo, Xinxia Peng, Michael G Katze

Bioinformatics· April 2012

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Genetic and epigenetic determinants of neurogenesis and myogenesis.
Abraham P Fong, Zizhen Yao, Jun Wen Zhong, Yi Cao, Walter L Ruzzo

Dev Cell· April 2012

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An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription.
Emily C Knouf, Kavita Garg, Jason D Arroyo, Yesenia Correa, Deepayan Sarkar, Walter L Ruzzo

Nucleic Acids Res· January 2012

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DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy.
Linda N Geng, Zizhen Yao, Lauren Snider, Abraham P Fong, Jennifer N Cech, Walter L Ruzzo

Dev Cell· January 2012

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Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.
Yi Cao, Zizhen Yao, Deepayan Sarkar, Michael Lawrence, Gilson J Sanchez, Walter L Ruzzo

Dev Cell· April 2010

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