ODNBase-a web database for antisense oligonucleotide effectiveness studies. - Michael C. Giddings; Olga V. Matveeva; John F. Atkins; Raymond F. Gesteland (Bioinform., 2000)

RECODE: a database of frameshifting, bypassing and codon redefinition utilized for gene expression. - Pavel V. Baranov; Olga L. Gurvich; Olivier Fayet; Marie Françoise Prère; W. Allen Miller; Raymond F. Gesteland; John F. Atkins; Michael C. Giddings (Nucleic Acids Res., 2001)

Computational identification of putative programmed translational frameshift sites. - Atul A. Shah; Michael C. Giddings; Jasmin B. Parvaz; Raymond F. Gesteland; John F. Atkins; Ivaylo P. Ivanov (Bioinform., 2002)

RECODE 2003. - Pavel V. Baranov; Olga L. Gurvich; Andrew W. Hammer; Raymond F. Gesteland; John F. Atkins (Nucleic Acids Res., 2003)

Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. - Olga V. Matveeva; Brian T. Foley; Vladimir A. Nemtsov; Raymond F. Gesteland; Senya Matsufuji; John F. Atkins; Aleksey Y. Ogurtsov; Svetlana A. Shabalina (BMC Bioinform., 2004)

ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting. - Michaël Bekaert; John F. Atkins; Pavel V. Baranov (Bioinform., 2006)

Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs. - Michaël Bekaert; Ivaylo P. Ivanov; John F. Atkins; Pavel V. Baranov (BMC Bioinform., 2008)

Recode-2: new design, new search tools, and many more genes. - Michaël Bekaert; Andrew E. Firth; Yan Zhang; Vadim N. Gladyshev; John F. Atkins; Pavel V. Baranov (Nucleic Acids Res., 2010)

rRNA: mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments. - Patrick B. F. O'Connor; Gene-Wei Li; Jonathan S. Weissman; John F. Atkins; Pavel V. Baranov (Bioinform., 2013)