scholarly article | Q13442814 |
P50 | author | Sean Eddy | Q7440970 |
P2093 | author name string | T A Jones | |
R J Klein | |||
E Rivas | |||
P2860 | cites work | Gapped BLAST and PSI-BLAST: a new generation of protein database search programs | Q24545170 |
Transcription attenuation: once viewed as a novel regulatory strategy | Q24549083 | ||
Amino acid substitution matrices from protein blocks | Q24563220 | ||
Identification of novel small RNAs using comparative genomics and microarrays | Q24601229 | ||
Active conservation of noncoding sequences revealed by three-way species comparisons | Q24623668 | ||
The complete genome sequence of Escherichia coli K-12 | Q27860542 | ||
A computational screen for methylation guide snoRNAs in yeast | Q28137615 | ||
Novel intergenic repeats of Escherichia coli K-12 | Q28144655 | ||
Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, cartilage-hair hypoplasia | Q28201408 | ||
Regulation of RpoS by a novel small RNA: the characterization of RprA | Q28204998 | ||
Novel small RNA-encoding genes in the intergenic regions of Escherichia coli | Q28205853 | ||
CRITICA: coding region identification tool invoking comparative analysis | Q29614364 | ||
Small RNAs in Escherichia coli. | Q33539353 | ||
Amino acid substitution matrices from an information theoretic perspective | Q33591465 | ||
Noncoding RNA genes | Q33801550 | ||
An RNA thermometer | Q33856037 | ||
Methionine synthesis in Escherichia coli: effect of the MetR protein on metE and metH expression | Q33861223 | ||
Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence | Q33903990 | ||
Genomic strategies to identify mammalian regulatory sequences | Q34185992 | ||
Comparison of genomic DNA sequences: solved and unsolved problems | Q34237560 | ||
Human-mouse genome comparisons to locate regulatory sites | Q45161206 | ||
Calculating nucleic acid secondary structure | Q47853339 | ||
A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator | Q48047346 | ||
Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs | Q48698785 | ||
Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome | Q63433341 | ||
P433 | issue | 17 | |
P407 | language of work or name | English | Q1860 |
P921 | main subject | Escherichia coli | Q25419 |
comparative genomics | Q1147112 | ||
P1104 | number of pages | 5 | |
P304 | page(s) | 1369-1373 | |
P577 | publication date | 2001-09-01 | |
P1433 | published in | Current Biology | Q1144851 |
P1476 | title | Computational identification of noncoding RNAs in E. coli by comparative genomics | |
P478 | volume | 11 |
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