progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement

AE Darling, B Mau, NT Perna - PloS one, 2010 - journals.plos.org
Background Multiple genome alignment remains a challenging problem. Effects of
recombination including rearrangement, segmental duplication, gain, and loss can create a …

Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote

JA Eisen, RS Coyne, M Wu, D Wu, M Thiagarajan… - PLoS …, 2006 - journals.plos.org
The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology.
Like other ciliates, this species has separate germline and soma functions that are …

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii

JM Carlton, SV Angiuoli, BB Suh, TW Kooij, M Pertea… - Nature, 2002 - nature.com
Species of malaria parasite that infect rodents have long been used as models for malaria
disease research. Here we report the whole-genome shotgun sequence of one species …

A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions

GV Glazko, EV Koonin, IB Rogozin, SA Shabalina - Trends in Genetics, 2003 - cell.com
Noncoding DNA in the human–mouse orthologous intergenic regions contains 'islands' of
conserved sequences, the functions of which remain largely unknown. We hypothesized that …

The genome of model malaria parasites, and comparative genomics

J Carlton, J Silva, N Hall - Current issues in molecular biology, 2005 - mdpi.com
The field of comparative genomics of malaria parasites has recently come of age with the
completion of the whole genome sequences of the human malaria parasite Plasmodium …

A periodic pattern of mRNA secondary structure created by the genetic code

SA Shabalina, AY Ogurtsov… - Nucleic acids …, 2006 - academic.oup.com
Single-stranded mRNA molecules form secondary structures through complementary self-
interactions. Several hypotheses have been proposed on the relationship between the …

Expansion of the human μ-opioid receptor gene architecture: novel functional variants

SA Shabalina, DV Zaykin, P Gris… - Human molecular …, 2009 - academic.oup.com
The μ-opioid receptor (OPRM1) is the principal receptor target for both endogenous and
exogenous opioid analgesics. There are substantial individual differences in human …

Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3

R Chaudhary, B Gryder, WS Woods, M Subramanian… - Elife, 2017 - elifesciences.org
Thousands of long noncoding RNAs (lncRNAs) have been discovered, yet the function of
the vast majority remains unclear. Here, we show that a p53-regulated lncRNA which we …

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

JH Kim, AT Dilthey, R Nagaraja, HS Lee… - Nucleic acids …, 2018 - academic.oup.com
Despite the key role of the human ribosome in protein biosynthesis, little is known about the
extent of sequence variation in ribosomal DNA (rDNA) or its pre-rRNA and rRNA products …

Continuing Evolution of Burkholderia mallei Through Genome Reduction and Large-Scale Rearrangements

L Losada, CM Ronning, D DeShazer… - Genome biology and …, 2010 - academic.oup.com
Burkholderia mallei (Bm), the causative agent of the predominately equine disease
glanders, is a genetically uniform species that is very closely related to the much more …