Time-Space Tradeoffs Communication Complexity and Data Streams Verification of Software and Hardware Proof Complexity and Satisfiability Parallel and Distributed Computing Data Structures Circuit and PRAM Lower Bounds Other topics
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)