List of works - Walter L. Ruzzo

A Marfan syndrome gene expression phenotype in cultured skin fibroblasts

scientific article

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

scientific article

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

scientific article

A linear time algorithm for finding all maximal scoring subsequences

scientific article published in January 1999

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

scientific article published on January 2013

A new approach to bias correction in RNA-Seq

scientific article published on 28 January 2012

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 18 July 2017

Atherosclerotic plaque smooth muscle cells have a distinct phenotype

scientific article

Bone morphogenetic protein 4: potential regulator of shear stress-induced graft neointimal atrophy.

scientific article

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

scientific article published on August 2017

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

scientific article

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

scientific article published on 8 April 2013

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

scientific article

Concepts and introduction to RNA bioinformatics

scientific article published on January 2014

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

scientific article

De novo discovery of structured ncRNA motifs in genomic sequences

scientific article published on January 2014

De novo prediction of structured RNAs from genomic sequences

scientific article

Discriminative motif analysis of high-throughput dataset.

scientific article published on 25 October 2013

Finding non-coding RNAs through genome-scale clustering.

scientific article

Genetic and epigenetic determinants of neurogenesis and myogenesis.

scientific article

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

scientific article published on April 2010

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

scientific article

Improved gene selection for classification of microarrays

scientific article published on 01 January 2003

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

scientific article

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

scientific article published on 16 August 2012

Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments

scholarly article published 20 November 2016

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

scientific article

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote

scientific article

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

scientific article

Model-based clustering and data transformations for gene expression data ⬇️

scientific article published on October 1, 2001

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

scientific article published on 9 January 2009

Pre-mRNA secondary structure prediction aids splice site prediction.

scientific article

Principal component analysis for clustering gene expression data.

scientific article

Results on communication complexity classes

article by Tak Wah Lam & Walter L. Ruzzo published April 1992 in Journal of Computer and System Sciences

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

scientific article

Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana.

scientific article published on 12 July 2018

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

scientific article

The identification and functional annotation of RNA structures conserved in vertebrates.

scientific article published on 9 May 2017

Time-Space Tradeoffs for Undirected Graph Traversal by Graph Automata

Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae

scientific article published on March 2002

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

scientific article

Two Applications of Inductive Counting for Complementation Problems

scientific article (publication date: June 1989)

Validating clustering for gene expression data.

scientific article

List of works by Walter L. Ruzzo

A Marfan syndrome gene expression phenotype in cultured skin fibroblasts

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

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

A linear time algorithm for finding all maximal scoring subsequences

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

A new approach to bias correction in RNA-Seq

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

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

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

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

Atherosclerotic plaque smooth muscle cells have a distinct phenotype

Bone morphogenetic protein 4: potential regulator of shear stress-induced graft neointimal atrophy.

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

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

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

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

Concepts and introduction to RNA bioinformatics

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

De novo discovery of structured ncRNA motifs in genomic sequences

De novo prediction of structured RNAs from genomic sequences

Discriminative motif analysis of high-throughput dataset.

Finding non-coding RNAs through genome-scale clustering.

Genetic and epigenetic determinants of neurogenesis and myogenesis.

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

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

Improved gene selection for classification of microarrays

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

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

Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments

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

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote

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

Model-based clustering and data transformations for gene expression data ⬇️

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

Pre-mRNA secondary structure prediction aids splice site prediction.

Principal component analysis for clustering gene expression data.

Results on communication complexity classes

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

Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana.

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

The identification and functional annotation of RNA structures conserved in vertebrates.

Time-Space Tradeoffs for Undirected Graph Traversal by Graph Automata

Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae

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

Two Applications of Inductive Counting for Complementation Problems

Validating clustering for gene expression data.