Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis.
Associating transcription factors and conserved RNA structures with gene regulation in the human brain.
Inhibition of β-catenin signaling respecifies anterior-like endothelium into beating human cardiomyocytes.
Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes.
Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data.
Chapter 1 of Gorodkin, Ruzzo, 2014.
Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.
(Best Paper Award)
DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy.
An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription.
Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.
MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.
A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.
A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data.
Computational Complexity Theory
http://web.cs.ualberta.ca/~hoover/P-complete Updates and Errata
http://www.cs.armstrong.edu/greenlaw/research/PARALLEL/index.html See also: Greenlaw, Hoover, Miyano, Ruzzo, Shiraishi and Shoudai: The Parallel Computation Project.
http://dx.doi.org/10.1137/0218084 Erratum: SIAM J. Comput. 18(6): 1283 (1989)