Evolutionary genomics of nucleo-cytoplasmic large DNA viruses

LM Iyer, S Balaji, EV Koonin, L Aravind - Virus research, 2006 - Elsevier
A previous comparative-genomic study of large nuclear and cytoplasmic DNA viruses
(NCLDVs) of eukaryotes revealed the monophyletic origin of four viral families: poxviruses …

Metabolite damage and its repair or pre-emption

CL Linster, E Van Schaftingen, AD Hanson - Nature chemical biology, 2013 - nature.com
It is increasingly evident that metabolites suffer various kinds of damage, that such damage
happens in all organisms and that cells have dedicated systems for damage repair and …

SCOP2 prototype: a new approach to protein structure mining

A Andreeva, D Howorth, C Chothia… - Nucleic acids …, 2014 - academic.oup.com
We present a prototype of a new structural classification of proteins, SCOP2 (http://scop2.
mrc-lmb. cam. ac. uk/), that we have developed recently. SCOP2 is a successor to the …

Data growth and its impact on the SCOP database: new developments

A Andreeva, D Howorth, JM Chandonia… - Nucleic acids …, 2007 - academic.oup.com
Abstract The Structural Classification of Proteins (SCOP) database is a comprehensive
ordering of all proteins of known structure, according to their evolutionary and structural …

Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation‐specific genes

MY Galperin, SL Mekhedov, P Puigbo… - Environmental …, 2012 - Wiley Online Library
Three classes of low‐G+ C Gram‐positive bacteria (Firmicutes), Bacilli, Clostridia and
Negativicutes, include numerous members that are capable of producing heat‐resistant …

Genetic Basis of Virulence Attenuation Revealed by Comparative Genomic Analysis of Mycobacterium tuberculosis Strain H37Ra versus H37Rv

H Zheng, L Lu, B Wang, S Pu, X Zhang, G Zhu, W Shi… - PloS one, 2008 - journals.plos.org
Tuberculosis, caused by Mycobacterium tuberculosis, remains a leading infectious disease
despite the availability of chemotherapy and BCG vaccine. The commonly used avirulent M …

Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics

MN Price, GM Zane, JV Kuehl, RA Melnyk, JD Wall… - PLoS …, 2018 - journals.plos.org
For many bacteria with sequenced genomes, we do not understand how they synthesize
some amino acids. This makes it challenging to reconstruct their metabolism, and has led to …

House cleaning, a part of good housekeeping

MY Galperin, OV Moroz, KS Wilson… - Molecular …, 2006 - Wiley Online Library
Cellular metabolism constantly generates by‐products that are wasteful or even harmful.
Such compounds are excreted from the cell or are removed through hydrolysis to normal …

Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1

H Neubauer, SE Clare, W Wozny, GP Schwall… - Breast Cancer …, 2008 - Springer
Introduction Breast tumors lacking the estrogen receptor-α (ER-α) have increased incidence
of resistance to therapy and poorer clinical prognosis. Methods Whole tissue sections from …

MazG – a regulator of programmed cell death in Escherichia coli

M Gross, I Marianovsky, G Glaser - Molecular microbiology, 2006 - Wiley Online Library
We have previously reported that mazEF, the first regulatable chromosomal 'addiction
module'located on the Escherichia coli chromosome, downstream from the relA gene, plays …