Searching in microbial genomes for encoded small proteins

Functional Characteristics of Small Proteins (70 Amino Acid Residues) Forming Protein-Nucleic Acid Complexes

(2012) Katarzyna Prymula et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

An expanding universe of small proteins

(2011) Errett C Hobbs et al.   CURRENT OPINION IN MICROBIOLOGY

Augmented Annotation of the Schizosaccharomyces pombe Genome Reveals Additional Genes Required for Growth and Viability

(2011) D. A. Bitton et al.   GENETICS

tsORFdb: Theoretical Small Open Reading Frames (ORFs) database and massProphet: Peptide Mass Fingerprinting (PMF) tool for unknown small functional ORFs

(2010) Hyoung-Sam Heo et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Missing genes in the annotation of prokaryotic genomes

(2010) Andrew S Warren et al.   BMC BIOINFORMATICS

Small Genes under Sporulation Control in the Bacillus subtilis genome

(2010) M. Schmalisch et al.   JOURNAL OF BACTERIOLOGY

“Fuzzy oil drop” model applied to individual small proteins built of 70 amino acids

(2010) Katarzyna Prymula et al.   JOURNAL OF MOLECULAR MODELING

Using comparative genome analysis to identify problems in annotated microbial genomes

(2010) M. S. Poptsova et al.   MICROBIOLOGY-SGM

Genome (re-)annotation and open-source annotation pipelines

(2010) Roland J. Siezen et al.   Microbial Biotechnology

Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays

(2010) Adnane Sellam et al.   GENOME BIOLOGY

sORF finder: a program package to identify small open reading frames with high coding potential

(2009) Kousuke Hanada et al.   BIOINFORMATICS

Paracrine signaling in a bacterium

(2009) D. Lopez et al.   GENES & DEVELOPMENT

Small RNAs and Small Proteins Involved in Resistance to Cell Envelope Stress and Acid Shock in Escherichia coli: Analysis of a Bar-Coded Mutant Collection

(2009) E. C. Hobbs et al.   JOURNAL OF BACTERIOLOGY

Small Stress Response Proteins in Escherichia coli: Proteins Missed by Classical Proteomic Studies

(2009) M. R. Hemm et al.   JOURNAL OF BACTERIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Revisiting the Saccharomyces cerevisiae predicted ORFeome

(2008) Q.-R. Li et al.   GENOME RESEARCH

Small membrane proteins found by comparative genomics and ribosome binding site models

(2008) Matthew R. Hemm et al.   MOLECULAR MICROBIOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology